|
Results from PredictProtein for t1
TOC for file t1
- The following information has been received by the server (TOC)
- MAXHOM alignment header (TOC)
- MAXHOM alignment (TOC)
- PHD information about accuracy (TOC)
- PHD predictions (TOC)
- GLOBE prediction of globularity (TOC)
END of TOC
BEG of results for file t1
rost@columbia.edu
ret concise
ret no prodom
ret no prosite
ret no coils
ret no seg
ret html 60
# paho_chick
MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
--- ------------------------------------------------------------
--- 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 97 36 0 0 36 P41337 PANCREATIC HORMONE (PANCR
paho_strca 89 96 36 0 0 36 P11967 PANCREATIC HORMONE (PANCR
paho_allmi 80 87 35 0 0 36 P06305 PANCREATIC HORMONE (PANCR
paho_ansan 72 73 36 0 0 36 P06304 PANCREATIC HORMONE (PANCR
neuy_sheep 60 78 35 0 0 36 P14765 NEUROPEPTIDE Y (NPY).
neuy_human 1RON 46 64 69 0 0 97 P01303 NEUROPEPTIDE Y PRECURSOR
neuy_chick 45 65 71 0 0 97 P28673 NEUROPEPTIDE Y PRECURSOR
neuy_pig 56 76 35 0 0 36 P01304 NEUROPEPTIDE Y (NPY).
neuy_rat 45 63 67 0 0 98 P07808 NEUROPEPTIDE Y PRECURSOR
neuy_xenla 42 62 69 0 0 97 P33689 NEUROPEPTIDE Y PRECURSOR.
pyy_pig 54 73 35 0 0 36 P01305 PEPTIDE YY (PYY).
neuy_rabit 54 75 35 0 0 36 P09640 NEUROPEPTIDE Y (NPY).
paho_canfa 41 52 71 1 1 93 P01299 PANCREATIC HORMONE PRECUR
npy_lamfl 40 53 70 1 3 104 P48097 NEUROPEPTIDE Y PRECURSOR
pyy_rat 39 53 75 1 2 98 P10631 PEPTIDE YY PRECURSOR (PYY
paho_human 39 54 72 1 2 95 P01298 PANCREATIC HORMONE PRECUR
neuy_ranri 51 73 35 0 0 36 P29949 (NPY).
pyy_amica 51 72 35 0 0 36 P29205 PEPTIDE YY-LIKE (PYY).
neuy_torma 38 57 71 0 0 98 P28674 NEUROPEPTIDE Y PRECURSOR
paho_rat 39 49 67 2 8 98 P06303 PANCREATIC HORMONE PRECUR
paho_mouse 38 50 69 2 6 100 P10601 PANCREATIC HORMONE PRECUR
pyy_human 35 52 79 0 0 97 P10082 PEPTIDE YY PRECURSOR (PYY
pyy_lamfl 38 50 63 1 1 93 P48098 PEPTIDE YY HOMOLOG PRECUR
paho_bovin 1BBA 35 49 77 1 2 131 P01302 PANCREATIC HORMONE PRECUR
paho_rante 49 66 35 0 0 36 P31229 PANCREATIC HORMONE (PANCR
paho_rabit 49 68 35 0 0 36 P41336 PANCREATIC HORMONE (PANCR
pyy_rajrh 49 71 35 0 0 36 P29206 PEPTIDE YY-LIKE (PYY).
pyy_lepsp 49 71 35 0 0 36 P09473 PEPTIDE YY-LIKE (PYY) (NE
pyy_oncki 49 70 35 0 0 36 P09474 PEPTIDE YY-LIKE (PYY).
neuy_oncmy 49 70 35 0 0 36 P29071 NEUROPEPTIDE Y (NPY).
pyy_bovin 36 54 67 0 0 97 P51694 PEPTIDE YY PRECURSOR (PYY
paho_cavpo 37 52 63 1 3 126 P13083 PANCREATIC HORMONE PRECUR
neuy_carau 34 52 71 0 0 96 P28672 NEUROPEPTIDE Y PRECURSOR
paho_didma 46 66 35 0 0 36 P18107 PANCREATIC HORMONE (PANCR
paho_macmu 46 66 35 0 0 36 P33684 PANCREATIC HORMONE (PANCR
paho_ranca 46 64 35 0 0 36 P15427 PANCREATIC HORMONE (PANCR
neuy_gadmo 46 69 35 0 0 36 P80167 NEUROPEPTIDE Y (NPY).
paho_pig 46 66 35 0 0 36 P01300 PANCREATIC HORMONE (PANCR
pyy_chick 43 65 37 0 0 37 P29203 PEPTIDE YY-LIKE (PYY).
paho_felca 37 56 52 0 0 66 P06884 PANCREATIC HORMONE PRECUR
paho_sheep 36 57 50 0 0 59 P01301 PANCREATIC HORMONE PRECUR
paho_equze 43 65 35 0 0 36 P38000 PANCREATIC HORMONE (PANCR
paho_erieu 43 65 35 0 0 36 P41335 PANCREATIC HORMONE (PANCR
paho_tappi 43 65 35 0 0 36 P39659 PANCREATIC HORMONE (PANCR
pyy_ranri 43 65 35 0 0 36 P29204 PEPTIDE YY-LIKE (PYY).
spyy_phybi 43 65 35 0 0 36 P80952 SKIN PEPTIDE TYROSINE-TYR
paho_cersi 43 65 35 0 0 36 P37999 PANCREATIC HORMONE (PANCR
ppy_lopam 40 56 40 0 0 69 P09475 PANCREATIC POLYPEPTIDE YG
---
--- MAXHOM ALIGNMENT: IN MSF FORMAT
--- ------------------------------------------------------------
--- 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!
--- ------------------------------------------------------------
---
--- Version of database searched for alignment:
--- SWISS-PROT release 38.0 (7/99) with 80000 proteins
---
TOP - BOTTOM -
MaxHom - MView
Identities computed with respect to: (1) t10
Colored by: consensus/70% and sequence
1 [ . . . . : . . ] 80
1 t10 100.0% MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
2 paho_chick 100.0% MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
3 paho_larar 94.4% -------------------------GPVQPTYPGDDAPVEDLVRFYNDLQQYLNVVTRHRY-------------------
4 paho_strca 88.9% -------------------------GPAQPTYPGDDAPVEDLVRFYDNLQQYLNVVTRHRY-------------------
5 paho_allmi 80.0% --------------------------PLQPKYPGDGAPVEDLIQFYDDLQQYLNVVTRPRF-------------------
6 paho_ansan 72.2% -------------------------GPSQPTYPGNDAPVEDLRFYYDNLQQYRLNVFRHRY-------------------
7 neuy_sheep 60.0% --------------------------PSKPDNPGDDAPAEDLARYYSALRHYINLITRQRY-------------------
8 neuy_human 46.4% ------SGLTLALSLLVCLGALAEAYPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
9 neuy_chick 45.1% ----WVSVLTFALSLLICLGTLAEAYPSKPDSPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
10 neuy_pig 57.1% --------------------------PSKPDNPGEDAPAEDLARYYSALRHYINLITRQRY-------------------
11 neuy_rat 44.8% --------LTLALSLLVCLGILAEGYPSKPDNPGEDAPAEDMARYYSALRHYINLITRQRYGKRSSPETLISDLL-----
12 neuy_xenla 42.0% ----WMSVLTLCLSMLICLGTFAEAYPSKPDNPGEDAPAEDMAKYYSALRHYINLITRQRYGKRSSPETMLSD-------
13 pyy_pig 54.3% --------------------------PAKPEAPGEDASPEELSRYYASLRHYLNLVTRQRY-------------------
14 neuy_rabit 54.3% --------------------------PSKPDNPGEDAPAEDMARYYSALRHYINLITRQRY-------------------
15 paho_canfa 39.4% -------LLLSACVALLLQPPLgrGAPLEPVYPGDDATPEQMAQYAAELRRYINMLTRPRYGKRDRGEMRDILEWGSP--
16 npy_lamfl 38.6% -----ARVWLCAIALCLLaaRGAAAFPNKPDSPGEDAPAEDLARYLSAVRHYINLITRQRYGKRTLTEPYVPEFI-----
17 pyy_rat 37.3% VAVRRPWPVMVAMLLVLLagALVDAYPAKPEAPGEDASPEELSRYYASLRHYLNLVTRQRYGKREVPAALFSKLL-----
18 paho_human 38.9% ------SLLLLStaLLLQPLLGAQGAPLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRYGKRHKEDTLAFSEWGSP--
19 neuy_ranri 51.4% --------------------------PSKPDNPGEDAPAEDMAKYYSALRHYINLITRQRY-------------------
20 pyy_amica 51.4% --------------------------PPKPENPGEDAPPEELARYYTALRHYINLITRQRY-------------------
21 neuy_torma 38.0% ----WLGVFTFAFCMLICIGTFADAYPSKPDNPGEGAPAEDLAKYYSALRHYINLITRQRYGKRSSPEALMMTDL-----
22 paho_rat 35.6% ------SLFLLStaLLLQPLQGAWGAPLEPMYPGDYATHEQRAQYETQLRRYINTLTRPRYGKRDE------DTAGLPG-
23 paho_mouse 35.6% ------SLFLVStaLLLQPLQGTWGAPLEPMYPGDYATPEQMAQYETQLRRYINTLTRPRYGKRAEE----ENTGGLPG-
24 pyy_human 35.4% VRRPWPALTTVLLALLVCLGALVDAYPIKPEAPGEDASPEELNRYYASLRHYLNLVTRQRYGKRDGPDTLLSKTFFPDG-
25 pyy_lamfl 37.5% ---RLAALALSVCAILCLGMHA-SAFPPKPDNPGDNASPEQMARYKAAVRHYINLITRQRYGKRALT-------------
26 paho_bovin 35.1% -AHRCLFLLLLStaLLLQPPLGALGAPLEPEYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDKEGTLDFLECGSP--
27 paho_rante 48.6% --------------------------PSEPHHPGDQATQDQLAQYYSDLYQYITFVTRPRF-------------------
28 paho_rabit 48.6% --------------------------PPEPVYPGDDATPEQMAEYVADLRRYINMLTRPRY-------------------
29 pyy_rajrh 48.6% --------------------------PPKPENPGDDAAPEELAKYYSALRHYINLITRQRY-------------------
30 pyy_lepsp 48.6% --------------------------PPKPENPGEDAPPEELAKYYSALRHYINLITRQRY-------------------
31 pyy_oncki 48.6% --------------------------PPKPENPGEDAPPEELAKYYTALRHYINLITRQRY-------------------
32 neuy_oncmy 48.6% --------------------------PVKPENPGEDAPTEELAKYYTALRHYINLITRQRY-------------------
33 pyy_bovin 35.8% ---SWPAMATVLLTLLVCLGELVDAYPAKPQAPGEHASPDELNRYYTSLRHYLNLVTRQRFGKRDFSEAL----------
34 paho_cavpo 34.8% ----WLLLLGTCMALLL---PEAWGAPLEPVYPGDDATPQQMAQYAAEMRRYINMLTRPRYGKSAEEDAL----------
35 neuy_carau 33.8% ----WTGWAACAFLLFVCLGTLTEGYPTKPDNPGEGAPAEELAKYYSALRHYINLITRQRYGKRSSADTLISDLL-----
36 paho_didma 45.7% --------------------------PQEPVYPGDDATPEQMAKYAAELRRYINRLTRPRY-------------------
37 paho_macmu 45.7% --------------------------PLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRY-------------------
38 paho_ranca 45.7% --------------------------PSEPHHPGDQATPDQLAQYYSDLYQYITFITRPRF-------------------
39 neuy_gadmo 45.7% --------------------------PIKPENPGEDAPADELAKYYSALRHYINLITRQRY-------------------
40 paho_pig 45.7% --------------------------PLEPVYPGDDATPEQMAQYAAELRRYINMLTRPRY-------------------
41 pyy_chick 43.2% ------------------------AYPPKPESPGDAASPEEIAQYFSALRHYINLVTRQRY-------------------
42 paho_felca 36.5% --------------------------PLEPVYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDRGETLDILEWGSP--
43 paho_sheep 36.0% ----------------------------EPEYPGDNATPEQMAQYAAELRRYINMLTRPRYGKRDKEGTLDFLECGSP--
44 paho_equze 42.9% --------------------------PMEPVYPGDNATPEQMAQYAAELRRYINMLTRPRY-------------------
45 paho_erieu 42.9% --------------------------PLEPVYPGDNATPEQMAHYAAELRRYINMLTRPRY-------------------
46 paho_tappi 42.9% --------------------------PLEPVYPGDNATPEQMAQYAAELRRYINMLTRPRY-------------------
47 pyy_ranri 42.9% --------------------------PPKPENPGEDASPEEMTKYLTALRHYINLVTRQRY-------------------
48 spyy_phybi 42.9% --------------------------PPKPESPGEDASPEEMNKYLTALRHYINLVTRQRY-------------------
49 paho_cersi 42.9% --------------------------PLEPVYPGDNATPEEMAQYAAELRRYINMLTRPRY-------------------
50 ppy_lopam 40.0% --------------------------PPKPETPGSNASPEDWASYQAAVRHYVNLITRQRYGXXSS--------------
consensus/100% ............................pP..PGp.As.pph..a.sth.pYh..lhR.Ra...................
consensus/90% .......................P.pP..PG-sAssEphspYhstLppYlNhlTR.RY.................
consensus/80% ......................P.cP..PG-sAssEphupYhstLR+YlNhlTR.RY..............
consensus/70% ....................P.cPp.PG-sAssEphApYhusLR+YINhlTR.RY..............
|
****************************************************************************
* *
* 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. *
* *
****************************************************************************
TOP - BOTTOM -
PHD
PHD predictions for t1
Different levels of data:
- PHD brief
- PHD normal
- PHDsec summary
overall your protein can be classified as:
mixed
given the following classes:
- 'all-alpha': %H > 45% AND %E < 5%
- 'all-beta': %H < 5% AND %E > 45%
- 'alpha-beta': %H > 30% AND %E > 20%
- 'mixed': all others
- Predicted secondary structure composition for your protein:
- Residue composition for your protein:
| %A: 8.8 | %C: 3.8 | %D: 5.0 | %E: 3.8 | %F: 1.2 |
| %G: 7.5 | %H: 1.2 | %I: 1.2 | %K: 0.0 | %L: 15.0 |
| %M: 2.5 | %N: 2.5 | %P: 11.2 | %Q: 3.8 | %R: 8.8 |
| %S: 7.5 | %T: 3.8 | %V: 6.2 | %W: 1.2 | %Y: 5.0 |
| AA : | amino acid sequence |
| PHD_sec: | PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD = PHD: Profile network prediction HeiDelberg |
| Rel_sec: | reliability index for PHDsec prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*' |
| SUB_sec: | subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header)
NOTE: for this subset the following symbols are used:
L: is loop (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 5 |
| | | |
| pH_sec: | 'probability' for assigning helix (1=high, 0=low) |
| pE_sec: | 'probability' for assigning strand (1=high, 0=low) |
| pL_sec: | 'probability' for assigning neither helix, nor strand (1=high, 0=low) |
| P_3_acc: | PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. |
| Rel_acc: | reliability index for PHDacc prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*' |
| SUB_acc: | subset of the PHDacc 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 |
| | | |
| PHD_acc: | PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%). |
PHD results (brief)
....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8
AA MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
PHD_sec HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHH
Rel_sec ** ************ ******************* **************** ************* ********
P_3_acc eeeebbbbbbbbbbbbbbeeeebee eeeee eeeebeeeebbebbbbb bbbbbbbbe bbeeeeeebbeeeeebeeee
Rel_acc * * * ****** * * * ** **
PHD results (normal)
....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8
AA MPPRWASLLLLACSLLLLAVPPGTAGPSQPTYPGDDAPVEDLIRFYNDLQQYLNVVTRHRYGRRSSSRVLCEEPMGAAGC
PHD_sec HHHHHHHHHHHHHH HHHHHHHHHHHHHHHHH
Rel_sec 99344667899999775148557799999899999999487899999999999963455558768757654478789999
SUB_sec LL...HHHHHHHHHHHH..LLLLLLLLLLLLLLLLLLL.HHHHHHHHHHHHHHHH..LLLLLLLLLLLLL..LLLLLLLL
P_3_acc eeeebbbbbbbbbbbbbbeeeebee eeeee eeeebeeeebbebbbbb bbbbbbbbe bbeeeeeebbeeeeebeeee
Rel_acc 31211425343546874000210210002011012131121533400071058235401101110232000112000210
SUB_acc .....b.b.b.bbbbbb........................b..b...b..bb..bb.......................
---
--- GLOBE: prediction of protein globularity
---
--- nexp = 44 (number of predicted exposed residues)
--- nfit = 42 (number of expected exposed residues
--- diff = 2.00 (difference nexp-nfit)
--- =====> your protein appears as compact, as a globular domain
---
---
--- GLOBE: further explanations preliminaryily in:
--- http://www.columbia.edu/~rost/Papers/1999_globe/paper.html
---
--- END of GLOBE
END of results for file t1
Quotes for methods
- PredictProtein:
PredicProtein: B Rost (1996) Methods in Enzymology, 266:525-539
- MaxHom:
MaxHom: C Sander R Schneider (1991) Proteins, 9:56-68
- Author: C Sander & R Schneider, schneider@lion-ag.de
- Contact: schneider@lion-ag.de
- Version: 1.99.04
- Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
- MView:
MView: N P Brown, C Leroy & C Sander (1998) Bioinformatics, 14:380-381
- Author: N Brown, nbrown@nimr.mrc.ac.uk
- Contact: nbrown@nimr.mrc.ac.uk
- Url: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
- Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.
- Version: 1.40.2
- Description: MView is a program converting multiple sequence alignments into fancy HTML formatted output.
- PHD:
B Rost (1996) Methods in Enzymology, 266:525-539
- Author: B Rost
- Version: 1.96
- Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments.
- PHDsec:
B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
- Author: B Rost
- Version: 1.96
- Description: PHD predicts secondary structure from multiple sequence alignments.
- PHDacc:
B Rost & C Sander (1994) Proteins, 20:216-226
- Author: B Rost
- Version: 1.96
- Description: PHD predicts per residue solvent accessibility from multiple sequence alignments.
- GLOBE:
B Rost (1998) unpublished
- Author: B Rost
- Version: 1.98.05
- Description: GLOBE predicts the globularity of a protein.
|
