ProDom output appended by default
Note: comments marked by "## COMMENT: "
The following information has been received by the server:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ return concise phdacc test seq from phd people run prodom #1ppt.pir ( 1ppt.hssp from: 1 to: 36 ) MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC ________________________________________________________________________________Result of PROSITE search (Amos Bairoch):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
Prosite Database -- Copyright: Amos Bairoch
ProSearch Software -- Release 1.2 -- Copyright: Lee Kolakowski
The following patterns are in < /home/phd/server/work/t-normal-32487.seqGCG >:
Access# From->To Name Doc#
_______ ________ ____________________ _________
PS00004 186->190 CAMP_PHOSPHO_SITE PDOC00004
PS00005 189->192 PKC_PHOSPHO_SITE PDOC00005
PS00009 184->188 AMIDATION PDOC00009
{PDOC00004}
{PS00004; CAMP_PHOSPHO_SITE}
{BEGIN}
cAMP- and cGMP-dependent protein kinase phosphorylation site
There has been a number of studies relative to the specificity of cAMP- and
cGMP-dependent protein kinases [1,2,3]. Both types of kinases appear to share
a preference for the phosphorylation of serine or threonine residues found
close to at least two consecutive N-terminal basic residues. It is important
to note that there are quite a number of exceptions to this rule.
-Consensus pattern: [RK](2)-x-[ST]
[S or T is the phosphorylation site]
-Last update: June 1988 / First entry.
[ 1] Fremisco J.R., Glass D.B., Krebs E.G.
J. Biol. Chem. 255:4240-4245(1980).
[ 2] Glass D.B., Smith S.B.
J. Biol. Chem. 258:14797-14803(1983).
[ 3] Glass D.B., El-Maghrabi M.R., Pilkis S.J.
J. Biol. Chem. 261:2987-2993(1986).
{END}
{PDOC00005}
{PS00005; PKC_PHOSPHO_SITE}
{BEGIN}
Protein kinase C phosphorylation site
In vivo, protein kinase C exhibits a preference for the phosphorylation of
serine or threonine residues found close to a C-terminal basic residue [1,2].
The presence of additional basic residues at the N- or C-terminal of the
target amino acid enhances the Vmax and Km of the phosphorylation reaction.
-Consensus pattern: [ST]-x-[RK]
[S or T is the phosphorylation site]
-Last update: June 1988 / First entry.
[ 1] Woodget J.R., Gould K.L., Hunter T.
Eur. J. Biochem. 161:177-184(1986).
[ 2] Kishimoto A., Nishiyama K., Nakanishi H., Uratsuji Y., Nomura H.,
Takeyama Y., Nishizuka Y.
J. Biol. Chem. 260:12492-12499(1985).
{END}
{PDOC00009}
{PS00009; AMIDATION}
{BEGIN}
Amidation site
The precursor of hormones and other active peptides which are C-terminally
amidated is always directly followed [1,2] by a glycine residue which provides
the amide group, and most often by at least two consecutive basic residues
(Arg or Lys) which generally function as an active peptide precursor cleavage
site. Although all amino acids can be amidated, neutral hydrophobic residues
such as Val or Phe are good substrates, while charged residues such as Asp or
Arg are much less reactive. C-terminal amidation has not yet been shown to
occur in unicellular organisms or in plants.
-Consensus pattern: x-G-[RK]-[RK]
[x is the amidation site]
-Last update: June 1988 / First entry.
[ 1] Kreil G.
Meth. Enzymol. 106:218-223(1984).
[ 2] Bradbury A.F., Smyth D.G.
Biosci. Rep. 7:907-916(1987).
{END}
________________________________________________________________________________
Result of ProDom domain search (Corpet, Gouzy, Kahn):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
--- ------------------------------------------------------------
--- Results from running BLAST against PRODOM domains
---
--- PLEASE quote:
--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database
--- of protein domain families. Nucleic Ac Res 26:323-326.
---
--- BEGIN of BLASTP output
BLASTP 1.4.7 [16-Oct-94] [Build 17:06:52 Oct 31 1994]
Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol.
215:403-10.
Query= prot (#) ppOld,1ppt.pir ( 1ppt.hssp from: 1 to: 36 ) t-prodom-norm
(80 letters)
Database: /home/phd/ut/prodom/prodom_34_2
53,597 sequences; 6,740,067 total letters.
Searching..................................................done
Smallest
Sum
High Probability
Sequences producing High-scoring Segment Pairs: Score P(N) N
29669 p34.2 (1) PAHO_CHICK // PANCREATIC HORMONE PRECURS... 135 7.8e-15 1
305 p34.2 (53) PAHO(24) PYY(13) NEUY(12) // PANCREATIC ... 121 5.4e-13 1
42848 p34.2 (1) MPRI_BOVIN // CATION-INDEPENDENT MANNOSE... 56 0.030 1
>29669 p34.2 (1) PAHO_CHICK // PANCREATIC HORMONE PRECURSOR (PANCREATIC
POLYPEPTIDE) (PP).
Length = 26
Score = 135 (63.0 bits), Expect = 7.8e-15, P = 7.8e-15
Identities = 26/26 (100%), Positives = 26/26 (100%)
Query: 1 MPPRWASLLLLACSLLLLAVPPGTAG 26
MPPRWASLLLLACSLLLLAVPPGTAG
Sbjct: 1 MPPRWASLLLLACSLLLLAVPPGTAG 26
>305 p34.2 (53) PAHO(24) PYY(13) NEUY(12) // PANCREATIC POLYPEPTIDE PP HORMONE
PRECURSOR PEPTIDE NEUROPEPTIDE Y PYY NPY
Length = 35
Score = 121 (56.5 bits), Expect = 5.4e-13, P = 5.4e-13
Identities = 19/35 (54%), Positives = 28/35 (80%)
Query: 27 PSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRY 61
P +P YPGDDAP E+L ++Y+ L+ Y+N++TR RY
Sbjct: 1 PPKPEYPGDDAPPEELAKYYSALRHYINLITRQRY 35
>42848 p34.2 (1) MPRI_BOVIN // CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
PRECURSOR (CI MAN-6-P RECEPTOR) (CI-MPR) (INSULIN-LIKE GROWTH FACTOR II
RECEPTOR).
Length = 42
Score = 56 (26.1 bits), Expect = 0.030, P = 0.030
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 2 PPRWASLLLLACSLLLLAVPPG 23
PPR LL L LLLL +PPG
Sbjct: 19 PPRCPLLLQLQLLLLLLLLPPG 40
Parameters:
E=0.1
B=500
V=500
-ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.324 0.140 0.445 same same same
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 80 80 0.10 63 3 11 22 0.19 29
Statistics:
Query Expected Observed HSPs HSPs
Frame MatID High Score High Score Reportable Reported
+0 0 53 (24.7 bits) 135 (63.0 bits) 3 3
Query Neighborhd Word Excluded Failed Successful Overlaps
Frame MatID Words Hits Hits Extensions Extensions Excluded
+0 0 2192 1370156 373828 986634 9694 233
Database: /home/phd/ut/prodom/prodom_34_2
Release date: unknown
Posted date: 12:24 PM MET DST May 06, 1998
# of letters in database: 6,740,067
# of sequences in database: 53,597
# of database sequences satisfying E: 3
No. of states in DFA: 516 (101 KB)
Total size of DFA: 151 KB (192 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Real: 00:00:00
Time to search database: 2.01u 0.08s 2.10t Real: 00:00:05
Total cpu time: 2.05u 0.10s 2.15t Real: 00:00:05
--- END of BLASTP output
--- ------------------------------------------------------------
---
--- Again: these results were obtained based on the domain data- --- base collected by Daniel Kahn and his coworkers in Toulouse.--- --- PLEASE quote: --- F Corpet, J Gouzy, D Kahn (1998). The ProDom database --- of protein domain families. Nucleic Ac Res 26:323-326. --- --- The general WWW page is on: ---- --------------------------------------- --- http://www.toulouse.inra.fr/prodom.html ---- --------------------------------------- --- --- For WWW graphic interfaces to PRODOM, in particular for your --- protein family, follow the following links (each line is ONE --- single link for your protein!!): ---
--- --- NOTE: if you want to use the link, make sure the entire line --- is pasted as URL into your browser! --- --- END of PRODOM --- ------------------------------------------------------------ ________________________________________________________________________________Note: Your protein has a homolologue of known structure in PDB!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PHD prediction are inferior to a prediction by homology, which is possible if protein with known tertiary structure exists in PDB. For the sequence you sent, there is a known homologue in in PDB. We append the alignment of your sequence to some seq- uences, among them the PDB entry. Predicting 3D structure for your sequence is a straightforward task by using, e.g., SWISS-MODEL (for the address see: http://www.embl-heidelberg.de/~rost/wwwServices.html Should you have sent a known structure to evaluate the PHD pre- diction, please mind that the performance of PHD is expected to be superior for proteins used for training the networks. The list of proteins used for training is: 256b_A, 2aat , 8abp , 6acn , 1acx , 8adh , 3ait , 1ak3_A, 2alp , 9api_A, 9api_B, 8atc_A, 8atc_B, 1azu , 3b5c , 1bbp_A, 1bds , 3blm , 1bmv_1, 1bmv_2, 4bp2 , 2cab , 7cat_A, 1cbh, 1cc5 , 2ccy_A, 1cd4 , 1cdt_A, 3cla , 3cln , 4cms , 4cpa_I, 6cpa , 6cpp , 4cpv , 1crn , 1cse_I, 6cts , 2cyp , 5cyt_R, 3dfr , 6dfr , 3ebx , 1eca , 5er2_E, 1etu , 1fc2_C, 1fc2_D, 1fdl_H, 1fdx , 1fkf , 2fnr , 2fxb , 1fxi_A, 4fxn , 3gap_A, 2gbp , 2gcr , 1gd1_O, 2gls_A, 2gn5 , 1gox , 1gp1_A, 4gr1, 1hds_B, 1hip , 6hir , 2hla_A, 3hla_B, 3hmg_A, 3hmg_B, 2hmz_A, 5hvp_A, 2i1b , 3icb , 7icd , 1il8_A, 9ins_B, 1l58 , 1lap, 2lbp , 5ldh , 2lh4 , 2lhb , 1lrd_3, 2ltn_A, 2ltn_B, 5lyz, 1mcp_L, 4mdh_A, 2mev_1, 2mev_3, 2mev_4, 2mhu , 1mrt , 2or1_L, 1ovo_A, 2pab_A, 1paz , 9pap , 2pcy , 4pfk , 3pgm , 2phh, 2pka_A, 2pka_B, 1pmb_A, 1ppt , 1prc_C, 1prc_H, 1prc_L, 1prc_M, 1pyp , 1r09_2, 1rbp , 1rhd , 4rhv_1, 4rhv_3, 4rhv_4, 1rnh, 3rnt , 7rsa , 2rsp_A, 2rus_A, 4rxn , 1s01 , 4sbv_A, 1sdh_A, 4sgb_I, 1sgt , 1sh1 , 2sns , 2sod_B, 2stv , 2taa_A, 2tbv_A, 2tgp_I, 1tgs_I, 3tim_A, 6tmn_E, 2tmv_P, 1tnf_A, 4ts1_A, 2tsc_A, 1ubq , 2utg_A, 9wga_A, 2wrp_R, 1wsy_A, 1wsy_B, 4xia_A For personal messages or questions to the PHD authors, send email to Predict-Help@EMBL-Heidelberg.DE Burkhard Rost EMBL, 69120 Heidelberg, Europe --- ------------------------------------------------------------ --- 3D homologue: the known structure that appeared to have sig- --- 3D homologue: nificant sequence identity to your protein is: --- 3D homologue: 1PPT, 1RON, 1BBA, . --- 3D homologue: Note: we do NOT check whether the similarity --- 3D homologue: is in the region for which structure has --- 3D homologue: been determined. Thus, please verify! --- ------------------------------------------------------------ --- Database used for sequence comparison: --- SEQBASE RELEASE 34.0 OF EMBL/SWISS-PROT WITH 59021 SEQUENCESThe alignment that has been used as input to the network is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
--- ------------------------------------------------------------
--- MAXHOM multiple sequence alignment
--- ------------------------------------------------------------
---
--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- ID : identifier of aligned (homologous) protein
--- STRID : PDB identifier (only for known structures)
--- PIDE : percentage of pairwise sequence identity
--- WSIM : percentage of weighted similarity
--- LALI : number of residues aligned
--- NGAP : number of insertions and deletions (indels)
--- LGAP : number of residues in all indels
--- LSEQ2 : length of aligned sequence
--- ACCNUM : SwissProt accession number
--- NAME : one-line description of aligned protein
---
--- MAXHOM ALIGNMENT HEADER: SUMMARY
ID STRID IDE WSIM LALI NGAP LGAP LEN2 ACCNUM NAME
paho_chick 1PPT 100 100 80 0 0 80 P01306 PANCREATIC HORMONE PRECUR
paho_larar 94 99 36 0 0 36 P41337 PANCREATIC HORMONE (PANCR
paho_strca 89 97 36 0 0 36 P11967 PANCREATIC HORMONE (PANCR
paho_allmi 78 90 36 0 0 36 P06305 PANCREATIC HORMONE (PANCR
paho_ansan 72 83 36 0 0 36 P06304 PANCREATIC HORMONE (PANCR
neuy_sheep 57 85 36 0 0 36 P14765 NEUROPEPTIDE Y (NPY).
neuy_pig 56 83 36 0 0 36 P01304 NEUROPEPTIDE Y (NPY).
neuy_human 1RON 40 69 80 0 0 97 P01303 NEUROPEPTIDE Y PRECURSOR
neuy_chick 40 71 80 0 0 97 P28673 NEUROPEPTIDE Y PRECURSOR
neuy_rabit 53 83 36 0 0 36 P09640 NEUROPEPTIDE Y (NPY).
pyy_pig 53 80 36 0 0 36 P01305 PEPTIDE YY (PYY).
neuy_rat 38 68 80 0 0 98 P07808 NEUROPEPTIDE Y PRECURSOR
neuy_xenla 36 70 80 0 0 97 P33689 NEUROPEPTIDE Y PRECURSOR.
pyy_amica 50 81 36 0 0 36 P29205 PEPTIDE YY-LIKE (PYY).
neuy_ranri 50 82 36 0 0 36 P29949 (NPY).
pyy_human 35 67 79 0 0 97 P10082 PEPTIDE YY PRECURSOR (PYY
neuy_torma 34 67 80 0 0 98 P28674 NEUROPEPTIDE Y PRECURSOR
pyy_lepsp 47 80 36 0 0 36 P09473 PEPTIDE YY-LIKE (PYY) (NE
neuy_oncmy 47 80 36 0 0 36 P29071 NEUROPEPTIDE Y (NPY).
pyy_oncki 47 80 36 0 0 36 P09474 PEPTIDE YY-LIKE (PYY).
paho_rante 47 76 36 0 0 36 P31229 PANCREATIC HORMONE (PANCR
paho_rabit 47 78 36 0 0 36 P41336 PANCREATIC HORMONE (PANCR
pyy_rajrh 47 80 36 0 0 36 P29206 PEPTIDE YY-LIKE (PYY).
pyy_rat 32 66 80 0 0 98 P10631 PEPTIDE YY PRECURSOR (PYY
paho_human 31 64 80 0 0 95 P01298 PANCREATIC HORMONE PRECUR
neuy_gadmo 44 80 36 0 0 36 P80167 NEUROPEPTIDE Y (NPY).
paho_macmu 44 77 36 0 0 36 P33684 PANCREATIC HORMONE (PANCR
paho_didma 44 77 36 0 0 36 P18107 PANCREATIC HORMONE (PANCR
paho_ranca 44 76 36 0 0 36 P15427 PANCREATIC HORMONE (PANCR
paho_pig 44 77 36 0 0 36 P01300 PANCREATIC HORMONE (PANCR
pyy_bovin 30 64 79 0 0 97 P51694 PEPTIDE YY PRECURSOR (PYY
neuy_carau 30 66 79 0 0 96 P28672 NEUROPEPTIDE Y PRECURSOR
paho_canfa 30 63 80 0 0 93 P01299 PANCREATIC HORMONE PRECUR
npy_lamfl 30 64 80 0 0 104 P48097 NEUROPEPTIDE Y PRECURSOR
paho_bovin 1BBA 30 63 80 0 0 131 P01302 PANCREATIC HORMONE PRECUR
pyy_chick 43 76 37 0 0 37 P29203 PEPTIDE YY-LIKE (PYY).
---
--- MAXHOM ALIGNMENT: IN MSF FORMAT
MSF of: /home/phd/dev/work/t-prodom-norm-17177.hssp from: 1 to: 80
/home/phd/dev/work/t-prodom-norm-17177.msfRet MSF: 80 Type: P 6-May-98 14:13:1 Check: 3364 ..
Name: t-prodom-nor Len: 80 Check: 8929 Weight: 1.00
Name: paho_chick Len: 80 Check: 8929 Weight: 1.00
Name: paho_larar Len: 80 Check: 2637 Weight: 1.00
Name: paho_strca Len: 80 Check: 2059 Weight: 1.00
Name: paho_allmi Len: 80 Check: 1391 Weight: 1.00
Name: paho_ansan Len: 80 Check: 2040 Weight: 1.00
Name: neuy_sheep Len: 80 Check: 9395 Weight: 1.00
Name: neuy_pig Len: 80 Check: 9430 Weight: 1.00
Name: neuy_human Len: 80 Check: 6685 Weight: 1.00
Name: neuy_chick Len: 80 Check: 7208 Weight: 1.00
Name: neuy_rabit Len: 80 Check: 9472 Weight: 1.00
Name: pyy_pig Len: 80 Check: 960 Weight: 1.00
Name: neuy_rat Len: 80 Check: 6895 Weight: 1.00
Name: neuy_xenla Len: 80 Check: 7175 Weight: 1.00
Name: pyy_amica Len: 80 Check: 50 Weight: 1.00
Name: neuy_ranri Len: 80 Check: 9164 Weight: 1.00
Name: pyy_human Len: 80 Check: 7370 Weight: 1.00
Name: neuy_torma Len: 80 Check: 5641 Weight: 1.00
Name: pyy_lepsp Len: 80 Check: 9695 Weight: 1.00
Name: neuy_oncmy Len: 80 Check: 66 Weight: 1.00
Name: pyy_oncki Len: 80 Check: 9742 Weight: 1.00
Name: paho_rante Len: 80 Check: 1819 Weight: 1.00
Name: paho_rabit Len: 80 Check: 54 Weight: 1.00
Name: pyy_rajrh Len: 80 Check: 9090 Weight: 1.00
Name: pyy_rat Len: 80 Check: 7817 Weight: 1.00
Name: paho_human Len: 80 Check: 7075 Weight: 1.00
Name: neuy_gadmo Len: 80 Check: 8874 Weight: 1.00
Name: paho_macmu Len: 80 Check: 9864 Weight: 1.00
Name: paho_didma Len: 80 Check: 9703 Weight: 1.00
Name: paho_ranca Len: 80 Check: 1052 Weight: 1.00
Name: paho_pig Len: 80 Check: 9552 Weight: 1.00
Name: pyy_bovin Len: 80 Check: 8609 Weight: 1.00
Name: neuy_carau Len: 80 Check: 5688 Weight: 1.00
Name: paho_canfa Len: 80 Check: 7058 Weight: 1.00
Name: npy_lamfl Len: 80 Check: 5405 Weight: 1.00
Name: paho_bovin Len: 80 Check: 6478 Weight: 1.00
Name: pyy_chick Len: 80 Check: 293 Weight: 1.00
//
1 50
t-prodom-nor MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
paho_chick MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
paho_larar .......... .......... .....GPVQP TYPGDDAPVE DLVRFYNDLQ
paho_strca .......... .......... .....GPAQP TYPGDDAPVE DLVRFYDNLQ
paho_allmi .......... .......... .....TPLQP KYPGDGAPVE DLIQFYDDLQ
paho_ansan .......... .......... .....GPSQP TYPGNDAPVE DLRFYYDNLQ
neuy_sheep .......... .......... .....YPSKP DNPGDDAPAE DLARYYSALR
neuy_pig .......... .......... .....YPSKP DNPGEDAPAE DLARYYSALR
neuy_human NKRLGLSGLT LALSLLVCLG ALAEAYPSKP DNPGEDAPAE DMARYYSALR
neuy_chick TMRLWVSVLT FALSLLICLG TLAEAYPSKP DSPGEDAPAE DMARYYSALR
neuy_rabit .......... .......... .....YPSKP DNPGEDAPAE DMARYYSALR
pyy_pig .......... .......... .....YPAKP EAPGEDASPE ELSRYYASLR
neuy_rat NKRMGLCGLT LALSLLVCLG ILAEGYPSKP DNPGEDAPAE DMARYYSALR
neuy_xenla NMRLWMSVLT LCLSMLICLG TFAEAYPSKP DNPGEDAPAE DMAKYYSALR
pyy_amica .......... .......... .....YPPKP ENPGEDAPPE ELARYYTALR
neuy_ranri .......... .......... .....YPSKP DNPGEDAPAE DMAKYYSALR
pyy_human VRRPWPALTT VLLALLVCLG ALVDAYPIKP EAPGEDASPE ELNRYYASLR
neuy_torma NMKFWLGVFT FAFCMLICIG TFADAYPSKP DNPGEGAPAE DLAKYYSALR
pyy_lepsp .......... .......... .....YPPKP ENPGEDAPPE ELAKYYSALR
neuy_oncmy .......... .......... .....YPVKP ENPGEDAPTE ELAKYYTALR
pyy_oncki .......... .......... .....YPPKP ENPGEDAPPE ELAKYYTALR
paho_rante .......... .......... .....APSEP HHPGDQATQD QLAQYYSDLY
paho_rabit .......... .......... .....APPEP VYPGDDATPE QMAEYVADLR
pyy_rajrh .......... .......... .....YPPKP ENPGDDAAPE ELAKYYSALR
pyy_rat VRRPWPVMVA MLLVLLACLG ALVDAYPAKP EAPGEDASPE ELSRYYASLR
paho_human RLCLSLLLLS TCVALLLQPL LGAQGAPLEP VYPGDNATPE QMAQYAADLR
neuy_gadmo .......... .......... .....YPIKP ENPGEDAPAD ELAKYYSALR
paho_macmu .......... .......... .....APLEP VYPGDNATPE QMAQYAADLR
paho_didma .......... .......... .....APQEP VYPGDDATPE QMAKYAAELR
paho_ranca .......... .......... .....APSEP HHPGDQATPD QLAQYYSDLY
paho_pig .......... .......... .....APLEP VYPGDDATPE QMAQYAAELR
pyy_bovin GRRSWPAMAT VLLTLLVCLG ELVDAYPAKP QAPGEHASPD ELNRYYTSLR
neuy_carau NMKMWTGWAA CAFLLFVCLG TLTEGYPTKP DNPGEGAPAE ELAKYYSALR
paho_canfa CRCLFLLLLS ACVALLLQPP LGTRGAPLEP VYPGDDATPE QMAQYAAELR
npy_lamfl GSARVWLCAI ALCLLASSCA RGAAAFPNKP DSPGEDAPAE DLARYLSAVR
paho_bovin HRCLFLLLLS TCVALLLQPP LGALGAPLEP EYPGDNATPE QMAQYAAELR
pyy_chick .......... .......... ....AYPPKP ESPGDAASPE EIAQYFSALR
51 80
t-prodom-nor QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
paho_chick QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
paho_larar QYLNVVTRHR Y......... ..........
paho_strca QYLNVVTRHR Y......... ..........
paho_allmi QYLNVVTRPR F......... ..........
paho_ansan QYRLNVFRHR Y......... ..........
neuy_sheep HYINLITRQR Y......... ..........
neuy_pig HYINLITRQR Y......... ..........
neuy_human HYINLITRQR YGKRSSPETL ISDLLMREST
neuy_chick HYINLITRQR YGKRSSPETL ISDLLLREST
neuy_rabit HYINLITRQR Y......... ..........
pyy_pig HYLNLVTRQR Y......... ..........
neuy_rat HYINLITRQR YGKRSSPETL ISDLLMREST
neuy_xenla HYINLITRQR YGKRSSPETM LSDVWWRENT
pyy_amica HYINLITRQR Y......... ..........
neuy_ranri HYINLITRQR Y......... ..........
pyy_human HYLNLVTRQR YGKRDGPDTL LSKTFFPDG.
neuy_torma HYINLITRQR YGKRSSPEAL MMTDLMLREN
pyy_lepsp HYINLITRQR Y......... ..........
neuy_oncmy HYINLITRQR Y......... ..........
pyy_oncki HYINLITRQR Y......... ..........
paho_rante QYITFVTRPR F......... ..........
paho_rabit RYINMLTRPR Y......... ..........
pyy_rajrh HYINLITRQR Y......... ..........
pyy_rat HYLNLVTRQR YGKREVPAAL FSKLLFTDDS
paho_human RYINMLTRPR YGKRHKEDTL AFSEWGSPHA
neuy_gadmo HYINLITRQR Y......... ..........
paho_macmu RYINMLTRPR Y......... ..........
paho_didma RYINRLTRPR Y......... ..........
paho_ranca QYITFITRPR F......... ..........
paho_pig RYINMLTRPR Y......... ..........
pyy_bovin HYLNLVTRQR FGKRDFSEAL LSILLFPDR.
neuy_carau HYINLITRQR YGKRSSADTL ISDLLIGET.
paho_canfa RYINMLTRPR YGKRDRGEMR DILEWGSPHA
npy_lamfl HYINLITRQR YGKRTLTEPY VPEFIFQENR
paho_bovin RYINMLTRPR YGKRDKEGTL DFLECGSPHS
pyy_chick HYINLVTRQR Y......... ..........
________________________________________________________________________________
PHD: Profile fed neural network systems from HeiDelberg
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Prediction of:
secondary structure, by PHDsec
solvent accessibility, by PHDacc
and helical transmembrane regions, by PHDhtm
Author:
Burkhard Rost
EMBL, 69012 Heidelberg, Germany
Internet: Rost@EMBL-Heidelberg.DE
All rights reserved.
The network systems are described in:
PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599.
B Rost & C Sander: Proteins, 1994, 19, 55-72.
PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226.
PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533.
The resulting network (PHD) prediction is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________________________________________________________
PHD: Profile fed neural network systems from HeiDelberg
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Prediction of:
secondary structure, by PHDsec
solvent accessibility, by PHDacc
and helical transmembrane regions, by PHDhtm
Author:
Burkhard Rost
EMBL, 69012 Heidelberg, Germany
Internet: Rost@EMBL-Heidelberg.DE
All rights reserved.
The network systems are described in:
PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599.
B Rost & C Sander: Proteins, 1994, 19, 55-72.
PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226.
PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533.
Some statistics
~~~~~~~~~~~~~~~
Percentage of amino acids:
+--------------+--------+--------+--------+--------+--------+
| AA: | L | P | R | A | S |
| % of AA: | 15.0 | 11.3 | 8.8 | 8.8 | 7.5 |
+--------------+--------+--------+--------+--------+--------+
| AA: | G | V | Y | D | T |
| % of AA: | 7.5 | 6.3 | 5.0 | 5.0 | 3.8 |
+--------------+--------+--------+--------+--------+--------+
| AA: | Q | E | C | N | M |
| % of AA: | 3.8 | 3.8 | 3.8 | 2.5 | 2.5 |
+--------------+--------+--------+--------+--------+--------+
| AA: | W | I | H | F |
| % of AA: | 1.3 | 1.3 | 1.3 | 1.3 |
+--------------+--------+--------+--------+--------+
PHD output for your protein
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Wed May 6 14:13:19 1998
Jury on: 5 different architectures (version 4.94_317 ).
Note: differently trained architectures, i.e., different versions can
result in different predictions.
About the protein
~~~~~~~~~~~~~~~~~
HEADER /home/phd/dev/work/t-prodom-norm-17177.f
COMPND
SOURCE
AUTHOR
SEQLENGTH 80
NCHAIN 1 chain(s) in t-prodom-norm-17177 data set
NALIGN 36
(=number of aligned sequences in HSSP file)
Abbreviations: PHDacc
~~~~~~~~~~~~~~~~~~~~~
sequence:
AA : amino acid sequence
SS : secondary structure
HEL: H=helix, E=extended (sheet), blank=other (loop)
solvent accessibility:
3st: relative solvent accessibility (acc) in 3 states:
b = 0-9%, i = 9-36%, e = 36-100%.
PHD: Profile network prediction HeiDelberg
Rel: Reliability index of prediction (0-9)
O_3: observed relative acc. in 3 states: B, I, E
note: for convenience a blank is used intermediate (i).
P_3: predicted relative accessibility in 3 states
10st:relative accessibility in 10 states:
= n corresponds to a relative acc. of n*n %
subset:
SUB: a subset of the prediction, for all residues with an expected
average correlation > 0.69 (tables in header)
note: for this subset the following symbols are used:
"I": is intermediate (for which above " " is used)
".": means that no prediction is made for this residue, as the
reliability is: Rel < 4
final prediction
protein: t-prodo length 80
....,....1....,....2....,....3....,....4....,....5....,....6
AA |MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHR|
3st: P_3 acc |eeeebbbbbbbbbbbbbbbbeebee eeeeeeeeeebeeeebbebbebbeebbbbbb e |
10st: PHD acc |997600000000000000006607957979977989067770070070066000000575|
Rel acc |944112135155668953211126313664843566114535263130621470353141|
subset: SUB acc |eee.....b.bbbbbbb......e...eeeee.eee..ee.b.e....b..bb..b..e.|
....,....7....,....8....,....9....,....10...,....11...,....12
AA |YGRRSSSRVLCEEPMGAAGC|
3st: P_3 acc | beeeeeebbbbeebbeeee|
10st: PHD acc |40767677000076007899|
Rel acc |11413155021041005669|
subset: SUB acc |..e...ee....e...eeee|
________________________________________________________________________________
The resulting prediction of globularity is:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ________________________________________________________________________________ --- GLOBE: prediction of protein globularity --- --- nexp = 43 (number of predicted exposed residues) --- nfit = 42 (number of expected exposed residues --- diff = 00. (difference nexp-nfit) --- =====> your protein appears as compact, as a globular domain --- --- END of GLOBE ________________________________________________________________________________