LOOPP parallel driver v5.0 (06/13/08 15:45 EDT) with LOOPP v3.0 (compiled Jul 11 2008 17:20:20)
[NEWSABLE] [HSHFL] [ENE] [NEWALICHOICE]
This is HTML output, the other options are plain text, CASP AL and CASP TS formats.
If an error occured during execution it is logged in plain text version only,
there is no need to look for an error if this file ends with 'DONE' statement.
STARTING:Sat Aug 09 06:35:45 2008 EST
INPUT:
sim_min = 40.0% minimum sequence identity (%)
sim_max = 80.0% maximum sequence identity (%)
len_dif = 20.0% maximum length difference (% of query sequence length)
between query and homolog
nmax = 1 maximum number of homologous sequences (including query sequence)
maxout = 5 maximum number of outputted matches
strict = 0 all alignments will be accepted from LOOPP results
for homologs; they will be translated to query sequence
alignments using BLAST results
casp = 5 maximum number of outputted matches in CASP format
align = 'g' only corresponding global alignments will be reported
maxdiff = 50.0% only alignments differing no more than 50.0% from the query
sequence will be reported, or when reject=0, corresponding local
alignments will be reported
reject = 1 alignments shorter more than 50.0% from the query sequence
will be rejected
seccut = 0.00 structures with sec. str. score below seccut will be rejected
secdb = 1 type of secondary structure description: 1 - DSSB, 0 - phi/psi map
tasktb = 11111111111111111111 type of initial calculations
pdbcut = 60.0% pdb sequence identity threshold (%)
pdbstop = 0 stop if PDB structure with similarity above pdbcut found
domains = 0 query sequence will be decomposed into putative domains if =1
maxall = 300 maximum number of models evaluated in the second stage
refstr = 0 if equal to 1 rmsd distances between all hits and a reference structure
will be reported
maxpdb = 5 number of top PDB hits added to the second stage scoring
maxdyn = 5 number of dynamic domain entries from database added to the second stage scoring
beautify = 0 use pdb beautifier
rmsdtables = 1 compute rmsd tables between hits
local LOOPP/BLAST database will be used
input file T0417
--> 189 residues, sequence name: T0417
Database: T:\CBSU\blastdb\20080108\nr
-> 72 homolog sequences with sequence identity from 40.0% to 80.0% satisfying length constraints found
-> 0 representatives will be used in search (nmax=1 including query sequence)
Histogram of all homolog sequences found by BLAST (e-value cutoff 0.01, length constr.) by sequence identity:
| 00%-10% | 10%-20% | 20%-30% | 30%-40% | 40%-50% | 50%-60% | 60%-70% | 70%-80% | 80%-90% | 90%-100% |
| 0 | 0 | 0 | 14 | 70 | 0 | 1 | 1 | 0 | 3 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 5.40 | 4.77 | 5.57 | 4.90 |
2 | 5.40 | 0.00 | 5.80 | 5.50 | 4.86 |
3 | 4.77 | 5.80 | 0.00 | 5.27 | 4.25 |
4 | 5.57 | 5.50 | 5.27 | 0.00 | 5.56 |
5 | 4.90 | 4.86 | 4.25 | 5.56 | 0.00 |
Similarity table for hits: percentage of chain fitting below 3Å RMSD (Cells are shaded according to similarity starting at 30%)
1 | 2 | 3 | 4 | 5 | |
1 | 100.00 | 57.05 | 29.63 | 43.95 | 19.62 |
2 | 57.05 | 100.00 | 30.13 | 57.79 | 20.78 |
3 | 29.63 | 30.13 | 100.00 | 31.85 | 39.24 |
4 | 43.95 | 57.79 | 31.85 | 100.00 | 38.85 |
5 | 19.62 | 20.78 | 39.24 | 38.85 | 100.00 |
Similarity table for hits: percentage of chain fitting below 6Å RMSD (Cells are shaded according to similarity starting at 50%)
1 | 2 | 3 | 4 | 5 | |
1 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
2 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
3 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
4 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
5 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
ALIGNMENTS
--> hit 1 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 28.00% helical, 40.00% extended, 32.00% loops/other (query: 28.04% 25.93% 46.03%)
SCOP classification:
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
2CNM_A not_found 66.66.66.66 NONE -48.663 0 1 79.89% 15.24% OPTM -515.135 -281.450 2.660 0.562 0.510 0.890 0.965 23.540 -44.5 4.100 101.500 -62.0 4.760 59.500 -113.0 3.240 15.000 -0.9 5.140 8.540 -47.0 5.660 28.230 11.8 3.650 3.880 -31.3 12.430 40.770 -30.9 15.370 23.260 -60.2 -30.000 38.000 -89.0 -30.000 39.000 -115.0 6.570 133.000 -67.0 12.450 60.000 -125.0 3.150 27.000 -11.0 5.980 11.000 -82.0 5.000 -9.5 -2.138 -24.1 0.000 -9.3e+061 5.000 -9.5 -0.022 -3.0 0.03 0.72
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
EEEEE---HHHHHHHHHHHHH--------HHHHHHHHHH- ---EEEEEE---EEEEEEEEEE------EEEEEEEEE-
Query: 26 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHH--AHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVH 103
Sbjct: 1 MNTISILSTTDLPAAWQIEQRAHAFPWS----EKTFFGNQGERYLNLKLTADDRMAAFAITQVVL----DEATLFNIAVD 72
-EEEEE-----HHHHHHHHHHH------ HHHHHH--------EEEEE--EEEEEEEEEEE- -EEEEEEEEE-
HHH----HHHHHHHHHHHHHH----EEEEEEE----HHHHHHHHHHHHH----EEEEEEE-------------EEEEE--
Query: 104 SRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGP 183
Sbjct: 73 PDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLG------FNEATIRRNYYPTAQGHEDAIIMAL-P 145
-------HHHHHHHHHHHHHHH----EEEEEEE---HHHHHHHHHH- -EEEEEEEEEEEE--EEEEEEEEEE E
------
Query: 184 FTHPPH 189
Sbjct: 146 ISMKLH 151
------
151 residues (79.89%) of query sequence aligned
--> hit 2 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 31.17% helical, 42.21% extended, 26.62% loops/other (query: 28.04% 25.93% 46.03%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Acyl-CoA N-acyltransferases (Nat)]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
d.108.1.1.22_A d.108.1.1 92.61.61.57 NONE -48.694 0 1 81.48% 17.86% OPTM -460.995 -301.800 1.954 0.635 0.525 0.875 0.946 19.460 -44.4 1.340 24.000 -15.5 2.160 46.500 -104.5 0.660 5.240 5.2 2.590 -1.240 -35.5 0.650 3.120 28.5 3.220 2.610 -25.9 8.830 21.880 -13.6 17.870 21.810 -63.3 -30.000 32.000 -91.0 -30.000 38.000 -115.0 2.260 18.000 15.0 5.550 46.000 -81.0 2.200 24.000 -21.0 4.900 12.000 -78.0 5.000 -5.7 -2.684 -20.5 0.000 -9.3e+061 5.000 -5.7 1.362 -0.3 0.13 0.61
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------------EEEEE---HHHHHHHHHHHHH--------HHHHHHHHHH----EEEEEE---EEEEEEEEEE------
Query: 14 PDISVAQPASALRYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPD 93
Sbjct: 3 EIIPVSTT-----LELRAADESHVPALHQLVLKNT---RKHVQGNILLHQRGYAKMYLIFCQN-EMAGVLSFNAIEPINK 73
-EEE---- EEEEE-----HHHHHHHHHH-- HHHHHHHHHHHHH---EEEEEEE-- EEEEEEEEEEEE----
EEEEEEEEE-HHH----HHHHHHHHHHHHHH--- -EEEEEEE----HHHHHHHHHHHHH----EEEEEEE------ --
Query: 94 VLFVWQVAVHSRARGHRLGRAMLGHILERQECRH-VRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFG-GA 171
Sbjct: 74 AAYIGYWLDES-FQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRN------HFTLEGCMKQAEYLNGD 146
EEEEEEEE--- -----HHHHHHHHHHHHHHHH----EEEEEEE---HHHHHHHHH- --EEEEEEEEEEEE--E
-----EEEEE
Query: 172 DHDDEMLLRI 181
Sbjct: 147 YHDVNMYARI 156
EEEEEEEEEE
154 residues (81.48%) of query sequence aligned
--> hit 3 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 23.23% helical, 23.23% extended, 53.54% loops/other (query: 28.04% 25.93% 46.03%)
SCOP classification:
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
2REE_A not_found 66.66.66.66 NONE -48.735 0 1 85.71% 14.20% OPTM -462.885 -202.290 1.353 0.584 0.514 0.771 0.940 22.610 -44.0 -1.560 -28.000 22.0 -0.360 7.000 -72.5 0.550 9.640 -23.8 1.910 -0.880 -55.7 0.770 12.850 -2.3 0.970 -4.440 -35.6 1.320 5.300 -24.7 7.340 10.670 -57.0 -30.000 4.000 -89.0 -30.000 22.000 -113.0 -0.290 -13.500 42.5 3.370 28.000 -69.0 1.560 16.000 -62.0 3.470 17.000 -95.0 5.000 -1.8 -1.165 -29.8 0.000 -9.3e+061 5.000 -1.7 0.000 0.8 0.14 0.85
alignment source: OPTM
EEEEE---HHHHHHHHHHHHH------- -HHHHHHHHHH----EEEEEE---EEEEEEEEEE---- -
Query: 26 RYHLRPPRRNDGAAIHQLVSECPPLDLN-SLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTR----------P-- 92
Sbjct: 227 YYNLRHPKIEDLRDLIALETLCWSENLQVDNEEIYRRIFKIPQGQFILELEDKIVGAIYSQRIDNPQLLDNKTCTQVPLL 306
EEEE------HHHHHHHHHHH--------HHHHHHHHHH-----EEEEE---EEEEEEEEEE------------------
-EEEEEEEEE-HHH----HHHHHHHHHHHHH H---- EEEEEEE----H HHHH HHH
Query: 93 -----DVLFVWQVAVHSRARGHRLGRAMLGHILERQ-ECRHV-RHLETTVGPDNQ------ASRR------------TFA 147
Sbjct: 307 HTESGVVVQLLAVNILPELQNQGLGDRLLEFMLQYCAQISGVEKVVAVTLCRNYPDYSPMPMAEYIHQKNESGLLVDPLL 386
-----EEEEEEEEE--------HHHHHHHHHHHHH-------EEEEEE------------HHHH------------HHHH
HHHHH----EEEEEEE-------------EEEEE------
Query: 148 GLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPFTHP 187
Sbjct: 387 RFHQIHGA--KIEKLLPGYRPKDWENQTCGVLVSYDIQHR 424
HHHH---E EEEEE-------------EEEEEE-----R
162 residues (85.71%) of query sequence aligned
--> hit 4 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 24.36% helical, 28.85% extended, 46.79% loops/other (query: 28.04% 25.93% 46.03%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Acyl-CoA N-acyltransferases (Nat)]
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
1MK4_A d.108.1.1 92.61.61.57 NONE -48.776 0 1 82.01% 15.92% OPTM -359.839 -214.940 3.094 0.622 0.514 0.908 0.908 23.560 -43.0 2.390 56.500 -35.5 3.150 29.500 -107.5 0.630 2.320 3.7 1.370 -0.470 -33.0 4.380 17.920 14.4 7.280 11.020 -35.5 12.190 27.790 -30.7 19.760 34.380 -76.2 -30.000 35.000 -94.0 -30.000 41.000 -124.0 5.560 115.000 -59.0 18.010 122.000 -163.0 4.140 43.000 -38.0 10.910 45.000 -103.0 5.000 -7.0 -0.620 -24.5 -69.000 263.0 5.000 -7.0 5.000 -3.2 0.15 0.87
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
EEE---HHHHHHHHHHHHH--- -----HHHHHHHHHH----EEEEEE---EEEEEEEEEE------EEEEEEEEE
Query: 28 HLRPPRRNDGAAIHQLVSECPP-----LDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAV 102
Sbjct: 4 DIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRL-----FFEHFQDTSFITSEHNS-MTGFLIGFQSQSDPETAYIHFSGV 77
EEE-----HHHHHHH----------------HH HHH-----EEEE----E EEEEEEEE------EEEEEEEEE-
-HHH----HHHHHHHHHHHHHH----EEEEEEE----HHHHHHHHHHHHH----EEE EEEE----------- --EEE
Query: 103 HSRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSE--QPFFDRQAFGGADHD-DEMLL 179
Sbjct: 78 HPDFRKMQIGKQLYDVFIETVKQRGCTRVKCVTSPVNKVSIAYHTKL----GFDIEKGTKTVNGISVFANYDGPGQDRVL 153
----HHHHHHHHHHHHHHHHH-----EEEEEE----HHHHHHHHH-- -EE----EEE--EEE-----------EEE
EE---
Query: 180 RIGPF 184
Sbjct: 154 FVKNI 158
EEE-I
155 residues (82.01%) of query sequence aligned
--> hit 5 [All-atom model (PDB)] [view all-atom model (PDB) with Chime] [PIR alignment file] [PDB file (backbone only)] [view PDB file (backbone only) with Chime] [hit list]
secondary structure: 23.91% helical, 36.23% extended, 39.86% loops/other (query: 28.04% 25.93% 46.03%)
SCOP classification:
name SCOP SCOP_stat confidence score homolog hits length seq. align ENE TE13 old CGenergy SIFT2 tma1 tma2 |-------OPTM------| |-------SEQ (global)-------| |-------SEQ (local)-------| |-------TRD (global)-------| |-------TRD (local)-------| |-------TRS (global)-------| |-------TRS (local)-------| |-------TSS (global)-------| |-------TSS (local)-------| |-------TSC (global)-------| |-------TSC (local)-------| |-------PSM (global)-------| |-------PSM (local)-------| |-------SRF (global)-------| |-------SRF (local)-------| |-------TBLS------| |-------KMER------| |-------CFTR------| |-------TBSS------| |-------SBLS------| sec. str.
(%) ident. src. all-atom all-atom score all-atom all-atom all-atom all-atom r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy zscore r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy r-energy energy pos. comp.
3BLN_A not_found 66.66.66.66 NONE -48.818 0 1 72.49% 12.66% OPTM -327.618 -258.010 1.370 0.599 0.501 0.822 0.929 13.550 -34.8 2.180 59.500 21.0 1.740 19.000 -75.5 1.690 6.820 18.6 3.960 2.460 -36.6 2.420 7.890 43.2 2.550 -0.930 -21.9 6.180 20.530 14.0 10.620 8.720 -47.0 -30.000 31.000 -74.0 -30.000 23.000 -102.0 4.120 58.000 15.0 4.350 36.000 -67.0 3.190 27.000 12.0 2.510 2.000 -61.0 5.000 -1.6 -0.030 -19.0 0.000 -9.3e+061 5.000 -1.6 5.000 0.8 0.14 0.71
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
EEE---HHHHHHHHHHHHH--------HHHHHHHHHH----EEEEEE---EEEEEEEEEE------EEEEEEEEE-HHH-
Query: 28 HLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRAR 107
Sbjct: 5 NVTKASIDDLDSIVHIDIDVIGNDSR--RNYIKHSIDEG-RCVIVKEDN-SISGFLTYDTNFF--DCTFLSLIIVSPTKR 78
EEE-----HHHHHHHHHHHH-----H HHHHHHHH--- EEEEEE--E EEEEEEEEEEE-- EEEEEEEEE------
---HHHHHHHHHHHHHH---- EEEEEEE----HHHHHHHHHHHHH----EEEEEEE-------------EEEEE----
Query: 108 GHRLGRAMLGHILERQECRHV--RHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPFT 185
Sbjct: 79 RRGYASSLLSY------LSHSPTQKIFSSTNESNESQ-----KVFNANGF--IRSGIVENLDEG----DPEIIFYTKKLR 141
--HHHHHHH-- ------EEEEEEE------H HHHH---E EEEEE------- -EEEEEEE---R
137 residues (72.49%) of query sequence aligned
DONE: Sat Aug 09 11:10:05 2008 EST