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 10 08:26:43 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 T0409
--> 103 residues, sequence name: T0409
Database: T:\CBSU\blastdb\20080108\nr
-> 0 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 | 1 | 0 | 0 | 0 | 0 | 1 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 12.02 | 13.51 | 10.30 | 12.63 |
2 | 12.02 | 0.00 | 14.13 | 14.60 | 13.66 |
3 | 13.51 | 14.13 | 0.00 | 11.12 | 12.64 |
4 | 10.30 | 14.60 | 11.12 | 0.00 | 11.55 |
5 | 12.63 | 13.66 | 12.64 | 11.55 | 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 | 23.81 | 25.29 | 20.69 | 22.35 |
2 | 23.81 | 100.00 | 20.21 | 21.28 | 19.57 |
3 | 25.29 | 20.21 | 100.00 | 17.53 | 20.43 |
4 | 20.69 | 21.28 | 17.53 | 100.00 | 22.58 |
5 | 22.35 | 19.57 | 20.43 | 22.58 | 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 | 39.29 | 35.63 | 36.78 | 30.59 |
2 | 39.29 | 100.00 | 30.85 | 34.04 | 44.57 |
3 | 35.63 | 30.85 | 100.00 | 36.08 | 34.41 |
4 | 36.78 | 34.04 | 36.08 | 100.00 | 61.29 |
5 | 30.59 | 44.57 | 34.41 | 61.29 | 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: 20.18% helical, 34.86% extended, 44.95% loops/other (query: 26.21% 25.24% 48.54%)
SCOP classification: [Alpha and beta proteins (a+b)]/[DNA clamp]
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.131.1.1.5_A d.131.1.1 104.11.11.5 GUESS -26.269 0 1 84.47% 10.34% OPTM -188.562 -168.430 0.763 0.538 0.478 0.536 0.729 7.820 -22.2 1.230 -13.500 1.5 1.380 26.500 -62.5 -0.340 -3.920 40.8 0.440 2.780 -16.0 -0.880 -9.640 55.5 -0.370 2.890 -11.3 3.150 16.330 16.9 8.170 2.370 -27.8 -30.000 14.000 -48.0 -30.000 -2.000 -56.0 1.210 4.000 36.0 1.680 12.000 -45.0 1.110 11.000 -10.0 2.010 11.000 -43.0 5.000 -0.6 1.958 -57.2 0.000 -9.3e+061 5.000 -0.6 5.000 5.0 0.03 0.69
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHH-- ----- EEEEEEE-----EEEEE--- -EEEE-HHHHHHHHHH------
Query: 17 REALQDIMQDIG----NSDDI--LAAVVLSATPGAVEAFRKNG---------------ETIRITGDGLKAAHRFLSNDPK 75
Sbjct: 131 TSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRLALAEEQIENEEEASFLLSLKSMKEVQNVLDNTTE 210
HHHHHHHHHH--------------EEEEEEE--EEEEEEE----EEEEEEE------EEEEEEHHHHHHHHHHHH-----
--HHHH----EEEEEE-----EEEE---
Query: 76 IGEKRIRPGALIRVKKTEKGSWQIVQLP 103
Sbjct: 211 ---------PTITVRYDGR-RVSLSTND 228
EEEEEE---E EEEE----
87 residues (84.47%) 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: 24.72% helical, 25.84% extended, 49.44% loops/other (query: 26.21% 25.24% 48.54%)
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.
1Y8X_B not_found 72.72.72.72 NONE -999.000 0 1 83.50% 11.70% OPTM -225.428 -129.540 1.072 0.484 0.226 0.800 0.832 5.090 -18.2 1.550 28.500 -30.5 1.270 0.500 -67.5 1.440 2.580 -2.0 0.090 1.520 -13.3 1.110 5.760 7.7 1.250 0.680 -12.2 6.700 26.330 -21.2 5.680 3.340 -26.7 -30.000 41.000 -64.0 -30.000 14.000 -65.0 2.240 38.000 -15.0 3.900 21.000 -59.0 2.660 17.000 -18.0 1.280 11.000 -34.0 5.000 -0.1 -2.171 -39.5 -24.000 126.0 5.000 -0.1 -0.745 -0.2 0.28 0.96
alignment source: OPTM
---------HHHHHHHHHHH-------EEEEEEE-----EEEEE----EEEE-HHHHHHHHHH--------HHHH----E
Query: 7 FLKLPKDLKDREALQDIMQDIGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGAL 86
Sbjct: 352 NIQFSPSAKLQEVLDYLTNSASLQKSPAITATLE---GKNRTLYQS------VTSIEERTRPNLSKTLK--ELGLVDGQE 420
EE------HHHHHHHHHH--------EEEEEE-- EEEE----- HHHHHHHHHHHH----- -------EE
EEEEE----- EEEE
Query: 87 IRVKKTEKGS---WQIV 100
Sbjct: 421 LAVADVTTPQTVLFKLH 437
EEE-------EEEEEE-
86 residues (83.50%) 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: 24.59% helical, 27.87% extended, 47.54% loops/other (query: 26.21% 25.24% 48.54%)
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.
2GW6_A not_found 72.72.72.72 NONE -999.000 0 1 95.15% 15.31% OPTM -286.864 -174.210 0.939 0.447 0.285 0.653 0.803 3.230 -19.5 0.400 22.500 4.0 0.090 -6.500 -56.0 -1.630 -7.930 20.3 0.650 2.690 -16.9 -1.480 -5.330 37.2 -0.480 -3.180 -10.2 4.740 14.280 -4.3 6.530 2.730 -27.1 -30.000 16.000 -61.0 -30.000 9.000 -66.0 -0.030 21.500 42.5 0.070 -2.000 -35.0 1.590 11.000 -13.0 4.170 12.000 -56.0 5.000 -0.6 -6.078 -61.9 0.000 -9.3e+061 5.000 -0.6 5.000 5.0 0.20 0.92
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
H---------HHHHHHHHHHH------- EEEEEEE----- EEEEE----EEEE-HHHHHHHHHH
Query: 6 AFLKLPKDLKDREALQDIMQDIGNSDDI------------LAAVVLSATPGA----VEAFRKNGETIRITGDGLKAAHRF 69
Sbjct: 16 MELDIG-DATQVYVAFLVYLDLMESKSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPITASLSHNRIREILKASRK 94
------ HHHHHHHHHHHHHHHH-----EEEEEEE----EEEEEEE--------EEEEEE------HHHHHHHHHHHHHH
--------HHHH----EEEEEE-----EEEE---
Query: 70 LSNDPKIGEKRIRPGALIRVKKTEKGSWQIVQLP 103
Sbjct: 95 LQGDPDL------PMSFTLAIVESDSTIVYYKLT 122
------- -EEEEEEE-----EEEEEEE-
98 residues (95.15%) 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: 15.75% helical, 40.16% extended, 44.09% loops/other (query: 26.21% 25.24% 48.54%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase]
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.
1F9Z_A d.32.1.1 104.6.6.1 NONE -999.000 0 1 94.17% 13.40% OPTM -243.163 -104.280 0.934 0.373 0.279 0.484 0.602 4.360 -19.6 -0.060 -3.500 9.0 1.500 -2.000 -74.5 0.520 7.990 20.5 0.050 0.180 -22.1 1.150 7.760 33.2 0.050 -1.610 -18.6 3.530 23.910 9.4 4.160 0.680 -25.8 -30.000 30.000 -52.0 -30.000 7.000 -56.0 2.930 45.500 15.0 2.700 17.000 -54.0 1.040 12.000 2.0 2.940 0.000 -45.0 5.000 0.6 2.772 -74.3 57.000 139.0 5.000 0.6 5.000 5.0 0.24 0.49
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
---------HHHHHHHHHHH-- -----EEEEEEE----- EEEEE--- -EEEE-HHHH
Query: 7 FLKLPKDLKDREALQDIMQDIG---------NSDDILAAVVLSATPGA----VEAFRKNG----------ETIRITGDGL 63
Sbjct: 3 LLHTMLRVGDLQRSIDFYTKVLGMKLLRTSENPEYKYSLAFVGYGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNA 82
-EEEEE---HHHHHHHHHH----EEEEEEEE----EEEEEEE--------EEEEEEE--------------EEEE---HH
HHHHHH---- ----HHHH----EEEEEE-----EEEE---
Query: 64 KAAHRFLSND---------PKIGEKRIRPGALIRVKKTEKGSWQIVQLP 103
Sbjct: 83 AEACEKIRQNGGNVTREAGPVKG----GTTVIAFVEDPDGYKIELIEEG 127
HHHHHHHH---EEEEEEEE---- --EEEEEE-----EEEEEE---
97 residues (94.17%) 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: 34.00% helical, 21.00% extended, 45.00% loops/other (query: 26.21% 25.24% 48.54%)
SCOP classification: [Alpha and beta proteins (a/b)]/[Aminoacid dehydrogenase-like, N-terminal domain]
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.
c.58.1.5.4_A c.58.1.5 8.2.2.2 NONE -999.000 0 1 89.32% 9.68% OPTM -111.858 -119.280 0.905 0.467 0.189 0.733 0.788 8.250 -18.8 0.320 -18.500 -15.0 -0.480 -7.500 -50.5 1.690 5.530 -10.8 1.280 1.720 -27.1 1.870 7.840 -0.3 0.870 0.030 -22.0 5.230 21.360 -25.0 8.040 8.100 -30.9 -30.000 25.000 -58.0 -30.000 21.000 -60.0 2.230 46.000 -2.0 3.560 19.000 -53.0 2.450 9.000 -31.0 1.830 4.000 -39.0 5.000 1.2 3.466 -41.1 -35.000 153.0 5.000 1.2 5.000 5.0 0.24 0.76
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
-------HHHHHHHHHHH-------EEEEEEE-- ---EEEEE----EEEE-HHHHHHHHHH------
Query: 9 KLPKDLKDREALQDIMQDIGNSDDILAAVVLSAT-------------PGAVEAFRKNGETIRITGDGLKAAHRFLSNDPK 75
Sbjct: 9 NPIAQSKSPLIQNKLAAQTHQT---MEYIAKLGDLDAFEQQLLAFFEEG--------AKGCNITSPFKERAYQLAD---E 74
------HHHHHHHHHHH----E EEEEEE-----HHHHHHHHHH--- -EEEE----HHHHHHH--E E
--HHHH----EEEEEE-----EEEE-
Query: 76 IGEKRIRPGALIRVKKTEKGSWQIVQ 101
Sbjct: 75 YSQRAKLAEACNTLKKLDDGKLYADN 100
-HHHHHH----EEEE-----EEEE--
92 residues (89.32%) of query sequence aligned
DONE: Sun Aug 10 10:58:24 2008 EST