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 00:09:26 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 = 200 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 T0400
--> 162 residues, sequence name: T0400
Database: T:\CBSU\blastdb\20080108\nr
-> 10 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 | 34 | 22 | 10 | 0 | 0 | 0 | 0 | 4 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 11.76 | 11.54 | 5.50 | 8.40 |
2 | 11.76 | 0.00 | 2.04 | 12.28 | 12.04 |
3 | 11.54 | 2.04 | 0.00 | 12.08 | 11.85 |
4 | 5.50 | 12.28 | 12.08 | 0.00 | 8.55 |
5 | 8.40 | 12.04 | 11.85 | 8.55 | 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 | 29.36 | 30.28 | 76.16 | 61.39 |
2 | 29.36 | 100.00 | 100.00 | 29.36 | 26.80 |
3 | 30.28 | 100.00 | 100.00 | 31.19 | 28.87 |
4 | 76.16 | 29.36 | 31.19 | 100.00 | 61.39 |
5 | 61.39 | 26.80 | 28.87 | 61.39 | 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 | 54.13 | 54.13 | 100.00 | 92.08 |
2 | 54.13 | 100.00 | 100.00 | 53.21 | 56.70 |
3 | 54.13 | 100.00 | 100.00 | 54.13 | 59.79 |
4 | 100.00 | 53.21 | 54.13 | 100.00 | 93.07 |
5 | 92.08 | 56.70 | 59.79 | 93.07 | 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: 25.00% helical, 28.75% extended, 46.25% loops/other (query: 41.36% 27.16% 31.48%)
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.
2Q7B_A not_found 39.39.39.39 NONE -40.765 0 1 98.15% 32.50% OPTM -752.594 -430.570 7.525 0.682 0.871 0.966 0.972 41.370 -61.1 14.790 296.500 -326.5 20.220 253.000 -340.5 3.640 12.160 -34.6 3.410 12.070 -40.6 8.950 45.610 -48.6 13.250 38.720 -61.0 15.420 74.040 -81.5 28.090 55.880 -89.5 -30.000 71.000 -122.0 -30.000 50.000 -122.0 29.450 501.000 -486.0 58.930 457.000 -507.0 7.780 84.000 -117.0 10.360 52.000 -126.0 5.000 -42.4 -2.627 -23.3 0.000 -9.3e+061 5.000 -42.3 -0.959 -21.3 0.71 0.64
alignment source: OPTM
-EEEEEE--HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH-----EEEEEEE---EEEEEEEEEE----EEEE
Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSAL 80
Sbjct: 7 GEIKEYENNPYHLAQLVDLINYCQNIEAKLDI-KAEQDDIFQIENYYQNRKGQFWIALEN-EKVVGSIALLRIDDKTAVL 84
-EEE----HHHHHHHHHHHHHHHH-------- --------HHHH------EEEEEEE-- EEEEEEEEEE----EEEEE
EEEEE-HHHH- -HHHHHHHHHHHHHHHH----EEEEEE---HHHHHHHHHH----EE--------------HHHEEHE
Query: 81 KKMFVDKGYRN--LKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYR 158
Sbjct: 85 KKFFTYPKYRGNPVRLGRKLFERFL-FARASKFTRIVLDTPEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVK 163
EEEE----------HHHHHHHH--H HHH----EEEEEEE---HHHHHHHH----EEE---------------EEEEEEE
E-
Query: 159 NL 160
Sbjct: 164 LL 165
-L
159 residues (98.15%) 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: 26.23% helical, 24.59% extended, 49.18% loops/other (query: 41.36% 27.16% 31.48%)
SCOP classification: [Alpha and beta proteins (a+b)]/[TTHA1528-like]
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.319.1.1.1_A d.319.1.1 76.2.2.2 NONE -41.064 0 1 67.28% 9.17% OPTM -354.999 -209.750 1.130 0.596 0.588 0.798 0.893 11.710 -29.5 -1.020 -38.000 64.5 -0.100 9.000 -51.0 0.400 -1.750 17.0 0.170 3.350 -41.4 1.780 -0.950 32.7 0.260 0.490 -31.8 4.200 9.830 12.2 11.090 9.700 -46.4 -30.000 26.000 -53.0 -30.000 15.000 -89.0 -0.170 -27.000 82.0 -0.370 1.000 -26.0 3.420 23.000 3.0 6.740 15.000 -68.0 5.000 -0.8 2.744 -48.9 0.000 -9.3e+061 5.000 -0.8 5.000 5.0 -0.11 0.65
alignment source: OPTM
HHHHHHHHHHHH-- ---EEEEEEE--- EEEEEEEEEE----EEEEEEEEE-HHHH--HHHHHHHHHHHHHHHH--
Query: 36 DQPDLENIEHNYLN---SGGQFWLAINNHQ--NIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQN 110
Sbjct: 9 PRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVPDAFGP----AFPGGEEALSELVGLLLAQG 84
HHHHHHHHHHH--------EEEEEEE---------EEEEEE----EEEEEEEE--- ---HHHHHHHHHHHHHH---
--EEEEEE--- HHHHHHHHHH----EE-------
Query: 111 IDGIYLGTIDK------FISAQYFYSNNGFREIKRGDLPS 144
Sbjct: 85 ARRFYEAVVSPGETALLDLPPEELLKRVAIANPTDPGIYL 124
-EEEEEEE-----------HHHHHHH----EE-------L
109 residues (67.28%) 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: 26.23% helical, 24.59% extended, 49.18% loops/other (query: 41.36% 27.16% 31.48%)
SCOP classification: [Alpha and beta proteins (a+b)]/[TTHA1528-like]
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.
1WN9_A d.319.1.1 76.2.2.2 NONE -41.170 0 1 67.28% 9.17% OPTM -352.418 -259.030 1.039 0.575 0.529 0.801 0.897 11.010 -28.9 -1.040 -39.500 71.5 0.310 12.000 -53.0 0.160 0.440 17.2 -0.250 -3.590 -25.6 1.450 0.470 34.2 0.080 -0.320 -17.2 4.140 11.900 12.5 11.310 10.600 -44.8 -30.000 26.000 -53.0 -30.000 15.000 -89.0 -0.180 -23.000 88.0 -0.230 2.000 -26.0 3.070 20.000 -3.0 5.130 12.000 -68.0 5.000 -0.8 2.744 -48.9 0.000 -9.3e+061 5.000 -0.8 5.000 5.0 -0.11 0.65
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHH-- ---EEEEEEE--- EEEEEEEEEE----EEEEEEEEE-HHHH--HHHHHHHHHHHHHHHH--
Query: 36 DQPDLENIEHNYLN---SGGQFWLAINNHQ--NIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQN 110
Sbjct: 9 PRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVPDAFGP----AFPGGEEALSELVGLLLAQG 84
HHHHHHHHHHH--------EEEEEEE---------EEEEEE----EEEEEEEE--- ---HHHHHHHHHHHHHH---
--EEEEEE--- HHHHHHHHHH----EE-------
Query: 111 IDGIYLGTIDK------FISAQYFYSNNGFREIKRGDLPS 144
Sbjct: 85 ARRFYEAVVSPGETALLDLPPEELLKRVAIANPTDPGIYL 124
-EEEEEEE-----------HHHHHHH----EE-------L
109 residues (67.28%) 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: 28.95% helical, 25.66% extended, 45.39% loops/other (query: 41.36% 27.16% 31.48%)
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.
2GE3_A d.108.1.1 76.60.60.56 NONE -41.480 0 1 93.21% 17.22% OPTM -540.319 -207.750 3.223 0.537 0.685 0.888 0.940 17.820 -36.6 2.560 9.000 -66.0 2.710 29.500 -98.5 4.190 15.800 -37.4 3.130 8.490 -39.6 4.060 21.360 -22.4 3.480 8.830 -27.1 10.990 57.430 -61.5 18.790 24.370 -63.4 -30.000 52.000 -108.0 -30.000 26.000 -108.0 5.850 81.000 -85.0 10.710 74.000 -119.0 9.430 93.000 -103.0 12.800 46.000 -108.0 5.000 -10.0 0.665 -34.8 0.000 -9.3e+061 5.000 -10.0 5.000 0.7 0.72 0.72
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-EEEEEE--HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH-- ---EEEEEEE---EEEEEEEEEE---
Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLN--SGGQFWLAINNHQNIVGTIGLIRLDN--- 75
Sbjct: 6 DTVTIKPIRAEHVESFHRALDAVSRERKYLSF--LEAPPLEAVRAFVLDIENDHPQFVAIADG-DVIGWCDIRRQDRATR 82
---EEEE-----HHHHHHHHHHHH-------- -----HHHHHHHHH-------EEEEEE-- EEEEEEEEEE------
-EEEEEEEEE-HHHH--HHHHHHHHHHHHHHHH----EEEEEE---HHHHHHHHHH----EE--------------
Query: 76 -NMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDV 151
Sbjct: 83 AHCGTLGG--ILPAYRNKGLGARLR-RTLDAAHEFGLHRIELSVHADNARAIALYEKIGFAHEGRARDAVSIDGHYI 156
--EEEE-- ---------HHHH-- HHHHHHHHH---EEE--EE---HHHHHHHHHH------EEEEEEE----EE
151 residues (93.21%) 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: 23.76% helical, 29.70% extended, 46.53% loops/other (query: 41.36% 27.16% 31.48%)
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.
1R57_A d.108.1.1 76.60.60.56 NONE -41.508 0 1 59.88% 17.82% OPTM -336.854 -175.990 1.411 0.563 0.454 0.868 0.876 7.780 -26.8 3.160 57.500 -12.0 3.310 38.500 -108.5 -0.070 -1.810 32.1 0.370 2.230 -22.4 4.040 9.420 38.2 3.770 9.420 -26.0 9.390 13.780 15.6 14.630 15.980 -44.7 -30.000 15.000 -30.0 -30.000 20.000 -78.0 3.590 51.000 27.0 5.550 45.000 -80.0 1.250 16.000 105.0 2.210 -1.000 -41.0 5.000 -6.3 -0.432 -19.9 39.000 147.0 5.000 -6.3 1.114 -3.0 -0.14 0.60
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-----EEEEEEE---EEEEEEEEEE----EEEEEEEEE-HHHH--HHHHHHHHHHHHHHHH----EEEEEE---HHHHHH
Query: 48 LNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQY 127
Sbjct: 6 IKQGENKFYIGDDENNALAEITYRFVDNNEINIDHTGVSDELGGQGVGKKLLKAVVEHARENNL-----KIIASCSFAKH 80
EEE--EEEEE-----EEEEEEEEE----EEEEEEEEE---------HHHHHHHHHHHHHHH--E EEE--HHHHHH
HHHH- ---EE-----------
Query: 128 FYSNN-GFREIKRGDLPSSFPK 148
Sbjct: 81 MLEKEDSYQDVYLGLEHHHHHH 102
HHH------------------H
97 residues (59.88%) of query sequence aligned
DONE: Sat Aug 09 03:36:33 2008 EST