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:Sun Aug 17 05:18:24 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 T0465
--> 157 residues, sequence name: T0465
Database: T:\CBSU\blastdb\20080108\nr
-> 1 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 | 5 | 9 | 1 | 0 | 0 | 0 | 3 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 22.60 | 18.58 | 21.37 | 19.25 |
2 | 22.60 | 0.00 | 16.41 | 18.87 | 19.19 |
3 | 18.58 | 16.41 | 0.00 | 16.15 | 17.34 |
4 | 21.37 | 18.87 | 16.15 | 0.00 | 11.48 |
5 | 19.25 | 19.19 | 17.34 | 11.48 | 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 | 10.32 | 13.04 | 11.69 | 11.69 |
2 | 10.32 | 100.00 | 13.57 | 10.39 | 9.74 |
3 | 13.04 | 13.57 | 100.00 | 10.95 | 12.41 |
4 | 11.69 | 10.39 | 10.95 | 100.00 | 20.13 |
5 | 11.69 | 9.74 | 12.41 | 20.13 | 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 | 19.35 | 28.26 | 22.08 | 23.38 |
2 | 19.35 | 100.00 | 24.29 | 22.73 | 24.68 |
3 | 28.26 | 24.29 | 100.00 | 24.82 | 35.77 |
4 | 22.08 | 22.73 | 24.82 | 100.00 | 45.45 |
5 | 23.38 | 24.68 | 35.77 | 45.45 | 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: 34.08% helical, 22.35% extended, 43.58% loops/other (query: 39.49% 15.29% 45.22%)
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.
1YWM_A not_found 60.60.60.14 NONE -999.000 0 1 98.73% 21.29% OPTM -254.744 -178.740 1.284 0.378 0.260 0.419 0.472 10.090 -23.8 4.330 109.000 -114.0 4.110 40.000 -138.5 1.410 -1.130 -1.3 0.210 0.370 -24.2 4.250 16.020 5.9 0.270 -2.050 -17.6 6.780 35.280 -20.8 7.190 15.480 -41.9 -30.000 50.000 -71.0 -30.000 32.000 -86.0 3.460 72.000 -36.0 3.050 20.000 -74.0 2.330 30.000 -39.0 2.130 25.000 -71.0 5.000 -1.3 0.257 -30.7 -54.000 291.0 5.000 0.1 -1.284 -0.4 0.73 0.75
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---- -----EHEHHEH--------- ----EEEEEEE--- --EEEEEE---HHHHHHHHHH-
Query: 1 MSEN---QNEKVYDLSFFMPGQTIDAEE---VEVPISKRFVDKEG-------------NVVPFIFKAITTDRIDELEKEN 61
Sbjct: 68 TSITKNIQNGNAYIDLYDVKLGKIDPLQLIVLEQGFTAKYVFRQGTKYYGDVSQLQSTGRASLTYNIFGED--------- 138
-----EE--EEEEEHHHHH---------EEE----EEEEEEEE--EEE---------EEEEEEEEEE----
--EEE-----------HHHHHHHEEHEHEE---- -HHHHHHH--- --HHHHHHHHH-----HHHHHHHHHHH---
Query: 62 TTYKNVKGRGRVKELDSQRFYARIAVETTVYPTF----KAKELREAYKT-EDPVEVAKRVLSVGGEYANWLNKAIEINGF 136
Sbjct: 139 -GLPHVKTDGQI---------DIVSVALTIYDSTTLRDKIEEVRTNANDPKWTEESRTEVLT----GLDTIKTDIDNNPK 204
----------- EEEEEEEEE--HHHHHHHHHHHHHH------HHHHHHHHHH HHHHHHHHHH----
-- HHHHHH HHHHHH-----
Query: 137 DD--------DLEDLE-----EAAKNLEHHHH 155
Sbjct: 205 TQTDIDSKIVEVNELEKLLVLKLAAALEHHHH 236
HHHHHHHHHHHHHHH-----HHHHHHH----H
155 residues (98.73%) 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: 31.58% helical, 18.05% extended, 50.38% loops/other (query: 39.49% 15.29% 45.22%)
SCOP classification: [Alpha and beta proteins (a+b)]/[SufE/NifU]
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.
1Q48_A d.224.1.2 35.1.1.1 NONE -999.000 0 1 80.89% 16.56% OPTM -123.576 -152.520 1.241 0.252 0.096 0.709 0.822 13.080 -25.5 4.930 67.500 -114.5 3.980 38.500 -119.0 1.280 3.140 1.3 1.060 1.190 -20.7 3.440 10.380 6.8 0.740 2.200 -13.7 7.920 31.200 -25.4 6.340 13.150 -37.1 -30.000 65.000 -87.0 -30.000 34.000 -87.0 6.310 63.500 -87.0 4.830 22.000 -87.0 2.820 16.000 5.0 1.150 5.000 -45.0 5.000 1.1 -1.740 -31.2 0.000 -9.3e+061 5.000 1.1 5.000 -0.4 0.76 0.79
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------EHEHHEH-------------EEEEEEE-----EEEEEE---HHHHHHHHHH---EEE-----------HHH
Query: 1 MSENQNEKVYDLSFFMPGQTIDAEEVEVPISKRFVDKEGNVVPFIFKAITTDRIDELEKENTTYKNVKGRGRVKELDSQR 80
Sbjct: 8 IDHYENPR--------NVGSLDKKDSNVGTGMVGAPACGDVMQLQIKVDDNG--------IIEDAKFKTYGCGSAIASSS 71
-------- ----------EEEEEEEE----EEEEEEEEE----- EEEEEEE-------HHHHHH
HHHHEEHEHEE-----HHHHHHH-----HHHHHHHHH----- HHHHHHHHHHH-----HHHHHHHHHHHH-------
Query: 81 FYARIAVETTVYPTFKAKELREAYKTEDPVEVAKRVLSVGGE--YANWLNKAIEINGFDDDLEDLEEAAKNLEHHHHHH 157
Sbjct: 72 LITE---------WVKGKSLEEAGAIK-NSQIAEELELPPVKVHCSILAEDAIKA------AIADYKAKQGLEHHHHHH 134
HHHH H----HHHH----H HHHHHHH-------HHHHHHHHHHHHH HHHHHH-----------H
127 residues (80.89%) 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: 23.19% helical, 34.06% extended, 42.75% loops/other (query: 39.49% 15.29% 45.22%)
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.
2JOE_A not_found 60.60.60.14 NONE -999.000 0 1 84.71% 20.00% OPTM -176.174 -213.650 1.079 0.487 0.285 0.802 0.807 9.560 -22.2 4.580 75.500 -117.0 5.550 58.500 -143.0 -0.000 0.800 -0.2 -0.450 -1.240 -20.9 2.900 11.250 3.1 -1.110 -1.460 -15.0 5.550 32.910 -19.6 6.200 10.350 -31.7 -30.000 50.000 -60.0 -30.000 17.000 -64.0 4.640 77.000 -69.0 4.360 40.000 -90.0 1.590 14.000 -15.0 3.090 20.000 -66.0 5.000 1.3 -0.329 -23.0 0.000 -9.3e+061 5.000 1.3 5.000 1.3 0.20 0.30
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------------EEEEEEE-----EEEEEE--- HHHHHHHHHH---EEE--- --------HHHHHHHEE
Query: 18 GQTIDAEEVEVPISKRFVDKEGNVVPFIFKAIT----------TDRIDELEKENTTYKNVKG-RGRVKELDSQRFYARIA 86
Sbjct: 7 SKKFSANLNGTEIAITYVYKGDKVLKQSSETKIQFASIGATTKEDAAKTLEPLSAKYKNIAGVEEKLTYTDT-----YAQ 81
EEEEEEE--EEEEEEEEEE--EEEEEEEEEEEE--------HHHHHHHHHHHH---------EEEEEE---E EEE
HEHEE-- ---HHHHHHH-----HHHHHHHHH-----HHHHHHHHHHH-----HHHHHHHHHHHH-------
Query: 87 VETTVYP-TFKAKELREAYKTEDPVEVAKRVLSVGGEYANWLNKAIEINGFDDDLEDLEEAAKNLEHHHHHH 157
Sbjct: 82 ENVTIDMEKVDFKALQGISGINVSAEDAKKGIT-----MAQMELVMKAAGFKEVKL---------EHHHHHH 139
EEEEE-----HHHH---------HHHHHH---H HHHHHHHHH----EEE-- ------H
133 residues (84.71%) 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: 44.32% helical, 3.41% extended, 52.27% loops/other (query: 39.49% 15.29% 45.22%)
SCOP classification: [Low resolution protein structures]/[RNA polymerase]
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.
1WCM_D i.8.1.1 2.2.2.2 NONE -999.000 0 1 98.09% 13.64% OPTM -191.287 -145.410 0.983 0.367 0.085 0.651 0.737 6.050 -27.6 1.590 30.500 -52.0 2.700 44.500 -115.5 1.400 1.130 -6.4 2.140 1.020 -24.0 1.190 3.980 8.5 0.120 -0.740 -13.8 5.190 19.920 -30.2 6.790 14.230 -46.9 -30.000 46.000 -96.0 -30.000 25.000 -100.0 1.440 27.000 -6.0 1.320 20.000 -64.0 2.210 23.000 2.0 1.130 3.000 -44.0 5.000 -0.1 -1.640 -23.9 -57.000 311.0 5.000 -0.1 0.869 0.6 0.74 0.67
alignment source: OPTM
---------EHEHHEH------------- EEEEEEE-----EEEEEE--- HHHHHHHHHH---EEE------
Query: 1 MSENQNEKVYDLSFFMPGQTIDAEEVEVP--ISKRFVDKEGNVVPFIFKAIT------TDRIDELEKENTTYKNVKGRGR 72
Sbjct: 4 AAAAAAAAAA------AAAAANAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFK-------RSQ 70
---------- ----------------------EEE-----EEE--------HHHHHHHHHHHHH HH-
-----HHHHHHHEEHEHEE----- HHHHHHH----- HHHHHHHHH-----HHHHHHHHHHH--
Query: 73 VKELDSQRFYARIAVETTVYPTFK-----AKELREAYKTED--PVEVAKRVLSVGGEYANWLNKAIEING---------- 135
Sbjct: 71 KKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLI 150
--------HHHHHHHHHHHHHH-----HHHHHHHHHHHH--------HHHHHHHHH--------HHHHHHH-----HHHH
---HHHHHHHHHHHH----
Query: 136 -------FDDDLEDLEEAAKNLEHHH 154
Sbjct: 151 PSLNNKISDDELERILKELSNLETLY 176
HHH---------HHHHHHHHHHHHHH
154 residues (98.09%) 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: 46.02% helical, 2.27% extended, 51.70% loops/other (query: 39.49% 15.29% 45.22%)
SCOP classification: [Low resolution protein structures]/[RNA polymerase]
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.
1Y1V_D i.8.1.1 2.2.2.2 NONE -999.000 0 1 98.09% 14.29% OPTM -179.869 -111.470 0.900 0.332 0.108 0.575 0.648 3.740 -24.7 1.660 21.500 -68.5 2.800 48.000 -121.0 1.100 3.530 -6.2 1.590 0.830 -23.5 1.320 5.000 6.1 -0.750 -1.380 -12.5 5.350 20.270 -31.5 6.650 15.500 -47.8 -30.000 39.000 -92.0 -30.000 16.000 -96.0 1.730 19.000 -17.0 1.200 16.000 -64.0 1.720 26.000 -26.0 0.780 -1.000 -43.0 5.000 -0.1 -1.363 -19.7 0.000 -9.3e+061 5.000 -0.0 0.964 0.0 0.68 0.61
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------EHEHHEH-------------EEEEEEE-----EEEEEE-- -HHHHHHHHHH---EEE--
Query: 1 MSENQNEKVYDLSFFMPGQTIDAEEVEVPISKRFVDKEGNVVPFIFKAI-------TTDRIDELEKENTTYKNVK----- 68
Sbjct: 10 TRRRRLKKVE------EEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKTREKELE 83
---------- ----------------EE-----EE--------HHHHHHHHHHHHHHHHHH-------HHHHHH
---------H HHHHHHEEHEHEE-----HHHHHHH---- -HHHHHHHHH-----HHHHHHHHHHH--
Query: 69 ---------GRGRVKELDS--QRFYARIAVETTVYPTFKAKELREAYKTE--DPVEVAKRVLSVGGEYANWLNKAIEING 135
Sbjct: 84 SIDVLLEQTTGGNNKDLKNTMQYLTNFSR----FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 159
HHHHHHHH-----HHHHHHHHHHHHH--- ----HHHHHHHHH------HHHHHH--------HHHHHHH-------
---HHHHHHHHHHHH----
Query: 136 --FDDDLEDLEEAAKNLEHHH 154
Sbjct: 160 KISDDELERILKELSNLETLY 180
--HHHHHHHHHHHHHH----Y
154 residues (98.09%) of query sequence aligned
DONE: Sun Aug 17 09:54:19 2008 EST