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:Wed Aug 13 02:16:28 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 T0446
--> 124 residues, sequence name: T0446
Database: T:\CBSU\blastdb\20080108\nr
-> 59 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 | 2 | 11 | 19 | 35 | 1 | 4 | 5 | 2 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 6.18 | 14.24 | 13.99 | 5.52 |
2 | 6.18 | 0.00 | 14.37 | 14.29 | 3.99 |
3 | 14.24 | 14.37 | 0.00 | 1.51 | 14.73 |
4 | 13.99 | 14.29 | 1.51 | 0.00 | 14.54 |
5 | 5.52 | 3.99 | 14.73 | 14.54 | 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 | 54.74 | 20.25 | 23.08 | 28.13 |
2 | 54.74 | 100.00 | 20.25 | 20.51 | 60.00 |
3 | 20.25 | 20.25 | 100.00 | 100.00 | 20.25 |
4 | 23.08 | 20.51 | 100.00 | 100.00 | 24.36 |
5 | 28.13 | 60.00 | 20.25 | 24.36 | 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 | 94.74 | 40.51 | 42.31 | 100.00 |
2 | 94.74 | 100.00 | 50.63 | 51.28 | 100.00 |
3 | 40.51 | 50.63 | 100.00 | 100.00 | 50.63 |
4 | 42.31 | 51.28 | 100.00 | 100.00 | 50.00 |
5 | 100.00 | 100.00 | 50.63 | 50.00 | 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: 13.56% helical, 35.59% extended, 50.85% loops/other (query: 28.23% 35.48% 36.29%)
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.
3B77_A not_found 58.58.58.12 NONE -31.137 0 1 76.61% 25.00% OPTM -358.672 -127.240 1.709 0.666 0.442 0.502 0.955 10.730 -33.8 1.160 6.000 35.0 8.420 78.500 -167.5 0.370 2.020 157.4 -0.390 1.210 -26.6 -0.340 -2.030 174.7 8.340 14.090 -35.0 -0.760 -12.780 111.1 14.470 14.180 -54.0 -30.000 -15.000 -12.0 -30.000 5.000 -83.0 -0.340 -5.000 114.0 8.410 74.000 -120.0 0.300 -5.000 67.0 2.520 6.000 -59.0 5.000 -10.0 -0.390 -26.5 0.000 -9.3e+061 5.000 -10.3 -1.180 -8.2 0.08 0.70
alignment source: OPTM
----EEEEEEEEE--EEEEE--EEEEE--------EEEEEEE------EEEEEE--------EEEEEEE----EEEEE--
Query: 28 GDNEQLALAYRVIRDMFVFTNKRLILIDKQGVTGKKVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQKDPLVKELK 107
Sbjct: 36 EDGEKIYFLIKSKTDEYCFTNLALVHLDGESASKRVLYRYPYAHYPIRHV-FETAGTVDLDVEIKFEIGGKHYSIDVDKK 114
----EEEEEE---EEEEEE--EEEEEE-------EEEEEE-----EE--- --------EEEEEEEE--EEEEEEEE---
---HHHHHHHHHHHHH
Query: 108 KGTDVVGIQKTIANFS 123
Sbjct: 115 QLEHVKDLYKALLAIA 130
HHHHHHHHHHHHHHHH
95 residues (76.61%) 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: 16.67% helical, 45.83% extended, 37.50% loops/other (query: 28.23% 35.48% 36.29%)
SCOP classification: [All beta proteins]/[PH domain-like barrel]
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.
b.55.1.5.6_A b.55.1.5 111.41.41.3 NONE -31.158 0 1 76.61% 15.79% OPTM -297.074 -149.100 0.620 0.594 0.517 0.797 0.918 10.860 -27.9 0.020 7.000 -7.0 -0.580 -4.500 -55.5 -0.230 -0.760 -4.0 -0.240 1.780 -19.3 -1.410 -5.910 14.2 1.790 5.920 -18.4 -0.790 -17.900 1.4 10.740 12.190 -42.2 -30.000 -18.000 -36.0 -30.000 6.000 -73.0 -0.490 -2.000 30.0 0.070 -2.000 -36.0 -1.060 -15.000 23.0 -0.920 -5.000 -30.0 5.000 1.3 1.095 -41.2 0.000 -9.3e+061 5.000 1.3 5.000 0.1 0.10 0.56
alignment source: OPTM
---EEEEEEE EE--EEEEE-- EEEEE--------EEEEEEE------EEEEEE--------EEEEEEE----EEEE
Query: 29 DNEQLALAYR---VIRDMFVFTNK-RLILIDKQGVTGKKVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQKDPLVK 104
Sbjct: 254 DKECFKCALGSSWIISVELAIGPEEGISYLTDKGAN----PTHLADFNQVQTIQYSNSEDKDRKGMLQLKIAGAPEPLTV 329
--EEEEEEE-----EEEEEEEE---EEEEE------ EEEEE----EEEEEEE--------EEEEEEE------EEE
E-----HHHHHHHHHHHHH
Query: 105 ELKKGTDVVGIQKTIANFS 123
Sbjct: 330 TAPSLTIAENMADLIDGYC 348
EE--HHHHHHHHHHHHHHH
95 residues (76.61%) 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: 0.00% helical, 47.96% extended, 52.04% loops/other (query: 28.23% 35.48% 36.29%)
SCOP classification: [All beta proteins]/[Immunoglobulin-like beta-sandwich]
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.
b.1.5.1.6_A b.1.5.1 111.46.4.4 NONE -31.305 0 1 63.71% 10.13% OPTM -214.375 -177.090 0.504 0.632 0.309 0.769 0.954 4.810 -22.7 0.430 15.500 9.5 -0.070 7.000 -53.0 0.720 -3.960 9.4 0.750 2.360 -28.3 0.360 -3.110 27.8 0.760 5.010 -21.5 1.460 2.470 9.7 9.710 2.620 -39.5 -30.000 3.000 -36.0 -30.000 1.000 -64.0 1.710 41.000 14.0 0.740 0.000 -40.0 -1.870 0.000 26.0 -1.880 1.000 -26.0 5.000 5.0 -4.831 -52.8 9.000 91.0 5.000 5.0 5.000 5.0 0.42 0.19
alignment source: OPTM
--EEEEEEEEE--EEEEE--EEEEE-------- EEEEEEE------EEEEEE--------EEEEEEE----EEEEE--
Query: 30 NEQLALAYRVIRDMFVFTNKRLILIDKQGVTGK--KVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQKDPLVKELK 107
Sbjct: 607 RKPVNVQMLFSNPLDEPVRDCVLMVEGSGLLLGNLKIDVPTLGPKERSRVRFDILPSRSGTKQLLADFSCNKFPAIKAML 686
--EEEEEEEE---------EEEEEE--------EEEEE-------EEEEEEEE-----EEEEEEEEEE------EEEEEE
-
Query: 108 K 108
Sbjct: 687 S 687
E
79 residues (63.71%) 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: 0.00% helical, 64.00% extended, 36.00% loops/other (query: 28.23% 35.48% 36.29%)
SCOP classification: [All beta proteins]/[Immunoglobulin-like beta-sandwich]
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.
b.1.5.1.2_A b.1.5.1 111.46.4.4 NONE -31.373 0 1 62.90% 12.82% OPTM -158.541 -122.350 0.620 0.663 0.319 0.734 0.935 1.840 -20.8 1.360 19.500 -8.5 2.050 27.000 -73.5 -0.360 -2.490 13.3 -0.810 0.050 -26.1 1.260 4.070 24.4 1.680 2.740 -24.1 4.590 1.820 2.6 10.810 5.830 -37.6 -30.000 5.000 -38.0 -30.000 -1.000 -63.0 1.220 23.000 15.0 1.880 8.000 -46.0 -1.520 -3.000 21.0 -1.340 1.000 -35.0 5.000 5.0 -1.881 -34.7 -8.000 111.0 5.000 5.0 1.114 -1.1 0.37 -0.13
alignment source: OPTM
--EEEEEEEEE--EEEEE--EEEEE-------- EEEEEEE------EEEEEE--------EEEEEEE--- -EEEEE--
Query: 30 NEQLALAYRVIRDMFVFTNKRLILIDKQGVTGK-KVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQK-DPLVKELK 107
Sbjct: 643 GSDMTVTVEFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELD 722
--EEEEEEEE------EEEEEEEEEE---EEEEEEEEEEE----EEEEEEEE-----EEEEEEEEEE----EEEEEEEEE
78 residues (62.90%) 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: 16.49% helical, 45.36% extended, 38.14% loops/other (query: 28.23% 35.48% 36.29%)
SCOP classification: [All beta proteins]/[PH domain-like barrel]
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.
b.55.1.1.6_A b.55.1.1 111.41.41.24 NONE -31.451 0 1 73.39% 10.31% OPTM -328.183 -177.620 0.657 0.591 0.533 0.739 0.853 5.780 -24.2 -0.340 1.000 -8.0 -0.200 11.500 -56.5 0.370 0.400 -7.8 1.080 3.710 -20.6 0.570 2.980 3.8 0.830 0.220 -15.0 0.660 -12.880 -5.8 8.080 2.880 -35.1 -30.000 -17.000 -40.0 -30.000 3.000 -71.0 -0.280 -16.000 17.0 0.600 8.000 -43.0 -1.400 -3.000 30.0 -0.540 -3.000 -29.0 5.000 0.5 -1.070 -62.5 0.000 -9.3e+061 5.000 0.5 5.000 5.0 0.14 0.57
alignment source: OPTM
-----EEEEEEEEE-- EEEEE--EEEEE--------EEEEEEE------EEEEEE--------EEEEEEE----EEE
Query: 27 MGDNEQLALAYRVIRD---MFVFTNKRLILIDKQGVTGKKVSYHSVPYKAITHFEVETAGTFDMDAELKLWISGQKDPLV 103
Sbjct: 555 LGKDCIMHGYMSKMGWQRRYFYLFPNRLEWRGEGEAPQ-----SLLTMEEIQSVEETQIK----ERKCLLLKIRGGKQFV 625
-----EEEEEEE---EEEEEEEE--EEEEE-------E EEE---EEEEEEEE--- -EEEEEEE----EEEE
EE-----HHHHHHHHHHHHH
Query: 104 KELKKGTDVVGIQKTIANFS 123
Sbjct: 626 LQCDSDPELVQWKKELRDAY 645
E---HHHHHHHHHHHHHHHH
91 residues (73.39%) of query sequence aligned
DONE: Wed Aug 13 05:22:09 2008 EST