LOOPP parallel driver v5.0 (06/13/08 15:45 EDT) with LOOPP v3.0 (compiled Jun 27 2008 14:09:10)
[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:Mon Jun 30 17:38:39 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 T0472
--> 110 residues, sequence name: T0472
Database: T:\CBSU\blastdb\20080108\nr
-> 63 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 | 0 | 19 | 23 | 21 | 0 | 0 | 2 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 13.52 | 13.73 | 13.23 | 10.53 |
2 | 13.52 | 0.00 | 8.48 | 10.69 | 15.46 |
3 | 13.73 | 8.48 | 0.00 | 9.63 | 15.13 |
4 | 13.23 | 10.69 | 9.63 | 0.00 | 16.06 |
5 | 10.53 | 15.46 | 15.13 | 16.06 | 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 | 32.43 | 25.68 | 29.73 | 45.59 |
2 | 32.43 | 100.00 | 23.33 | 20.41 | 17.98 |
3 | 25.68 | 23.33 | 100.00 | 26.67 | 29.11 |
4 | 29.73 | 20.41 | 26.67 | 100.00 | 21.84 |
5 | 45.59 | 17.98 | 29.11 | 21.84 | 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 | 60.81 | 47.30 | 56.76 | 67.65 |
2 | 60.81 | 100.00 | 53.33 | 58.16 | 38.20 |
3 | 47.30 | 53.33 | 100.00 | 53.33 | 39.24 |
4 | 56.76 | 58.16 | 53.33 | 100.00 | 35.63 |
5 | 67.65 | 38.20 | 39.24 | 35.63 | 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: 35.80% helical, 23.46% extended, 40.74% loops/other (query: 24.55% 33.64% 41.82%)
SCOP classification: [Alpha and beta proteins (a+b)]/[dsRBD-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.
1X48_A d.50.1.1 95.3.3.3 GUESS -27.708 0 1 67.27% 12.16% OPTM -170.952 -114.040 0.702 0.482 0.225 0.768 0.901 8.670 -23.2 -0.750 5.500 -3.0 0.710 10.500 -65.5 0.350 1.480 11.0 -0.080 0.730 -11.2 -0.810 -1.410 20.8 1.180 2.990 -10.5 1.650 -6.650 3.3 9.940 6.260 -30.9 -30.000 -12.000 -29.0 -30.000 1.000 -60.0 -0.490 -5.000 21.0 0.280 6.000 -38.0 -0.630 12.000 55.0 5.020 16.000 -43.0 5.000 -0.7 0.045 -50.3 0.000 -9.3e+061 5.000 -0.7 0.079 0.4 -0.11 0.57
alignment source: OPTM
----HHHHHHHHHHHHH-------EEEEE---- -EEEEEEE---EEEEE----- HHHHHHHHHHHHHH------
Query: 32 LYTGKSGAMNGIESVQTNSPIEARYAKEVAKND---KPYFNLKAANHQIIGTSQMYS---STAARDNGIKSVMENGKTTT 105
Sbjct: 1 GSSGSSGYIGLVNSFAQKKKLSVNYEQCEPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLAAKEAYQKLLKSPPKTA 80
-------HHHHHHHHHHH----EEEEE----------EEEEEEE---EEEEEEE--HHHHHHHHHHHHHHHHHH------
74 residues (67.27%) 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: 24.42% helical, 33.72% extended, 41.86% loops/other (query: 24.55% 33.64% 41.82%)
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.
2YY3_A not_found 55.55.55.55 GUESS -28.067 0 1 77.27% 13.00% OPTM -159.187 -95.620 0.809 0.378 0.246 0.778 0.866 6.890 -23.9 1.060 16.000 -2.5 1.400 19.500 -59.5 -1.340 -2.850 17.3 -0.590 -0.030 -11.3 -0.580 -2.450 27.5 -0.300 -0.550 -9.5 6.680 13.060 -5.4 7.610 1.830 -27.7 -30.000 9.000 -53.0 -30.000 2.000 -67.0 0.800 4.000 20.0 1.750 14.000 -45.0 1.210 28.000 -1.0 2.480 13.000 -43.0 5.000 -0.3 -1.563 -57.5 0.000 -9.3e+061 5.000 -0.3 5.000 0.5 0.18 1.00
alignment source: OPTM
----EEEEEE----EEEEE------HHHHHHHHHHHHH-------EEEEE-----EEEEEEE---EEEEE-- ---HHHH
Query: 11 SNDQFKFVLKAGNGEVILTSELYTGKSGAMNGIESVQTNSPIEARYAKEVAKNDKPYFNLKAANHQIIGTSQ-MYSSTAA 89
Sbjct: 2 SDFNLVGVIRVPT-------DPDVNLDELEEKLKKVIPEKYGLAKVEREPIAFG--LVALKF---YVLGRDEEGYS---- 65
----EEEEEE--- -----HHHHHHHHHHH-----EEEEEEEEE---- -EEEEE EEEE-------
HHHHHHHHHH------EEEE-
Query: 90 RDNGIKSVMENGKTTTIKDLT 110
Sbjct: 66 FDEVAEKFEEVENVESAEVET 86
HHHHHHHHHH-------EEEE
85 residues (77.27%) 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: 34.62% helical, 25.64% extended, 39.74% loops/other (query: 24.55% 33.64% 41.82%)
SCOP classification: [Alpha and beta proteins (a+b)]/[Ferredoxin-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.58.11.1.3_A d.58.11.1 95.37.2.2 GUESS -28.141 0 1 66.36% 7.78% OPTM -125.217 -103.160 0.524 0.341 0.122 0.729 0.821 8.970 -24.3 0.730 13.000 24.5 2.080 -0.500 -59.0 -0.180 0.080 28.0 -0.690 0.710 -11.2 0.010 -0.040 40.8 1.280 2.500 -11.3 4.610 14.220 13.5 5.560 -1.660 -20.2 -30.000 18.000 -41.0 -30.000 2.000 -53.0 0.290 9.000 50.0 1.020 5.000 -37.0 1.130 16.000 26.0 2.270 3.000 -37.0 5.000 0.2 -4.065 -64.7 -20.000 126.0 5.000 0.2 -0.678 -1.3 0.04 0.64
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
----EEEEE------HHHHHHHHHHHHH-------EEEEE-----EEEEEEE---EEEEE-----HHHHHHHHHHHHHH-
Query: 21 AGNGEVILTSELYTGKSGAMNGIESVQTNSPIEARYAKEVAKNDKPYFNLKAANHQIIGTSQMYSSTAARDNGIKSVMEN 100
Sbjct: 486 SPVVQVAVEVKNANDLPKLVEGLKRLSKSDPC---VLTYMSES---------GEHIVAGTG-----ELHLEICLQDLEHD 548
--EEEEEEE-----HHHHHHHHHHHHHH---- EEEE---- -EEEEE--H HHHHHHHHHHHH--
-----EEEE-
Query: 101 GKTTTIKDLT 110
Sbjct: 549 HAGVPLKISP 558
----EEEE--
73 residues (66.36%) 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: 41.07% helical, 26.79% extended, 32.14% loops/other (query: 24.55% 33.64% 41.82%)
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.
2IDL_A not_found 55.55.55.55 GUESS -28.295 0 1 89.09% 14.29% OPTM -146.958 -187.520 1.111 0.471 0.203 0.713 0.813 6.510 -25.2 0.300 12.000 -16.5 -0.090 2.000 -54.5 0.060 -1.190 -5.2 -0.510 0.480 -14.2 1.130 1.690 1.3 -1.300 0.120 -8.6 8.170 44.860 -34.8 13.660 5.970 -34.8 -30.000 40.000 -74.0 -30.000 15.000 -74.0 3.330 42.000 -22.0 1.400 11.000 -44.0 2.770 21.000 -33.0 1.710 5.000 -38.0 5.000 5.0 -1.449 -48.8 0.000 -9.3e+061 5.000 -0.6 5.000 0.2 0.07 0.53
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--EEEEEE---- EEEEE------ HHHHHHHHHHHHH-------EEEEE-----EEEEEEE---EE
Query: 13 DQFKFVLKAGNG----EVILTSELYTG-----------KSGAMNGIESVQTNSPIEARYAKEVAKNDKPYFNLKAANHQI 77
Sbjct: 2 AMIQAVFERAEDGELRSAEITGHAESGEYGLDVVCASVSTLAINFINSIEKFAGYEP--ILELNEDEGGYLMVEIP---- 75
--EEEEEEE-----EEEEEEE---------HHHHHHHHHHHHHHHHHHHHHH----- EEEEE-----EEEEE--
EEE-----H HHHHHHHHHHHHH------EEEE-
Query: 78 IGTSQMYSS---------TAARDNGIKSVMENGKTTTIKDLT 110
Sbjct: 76 ----KDLPSHQREMTQLFFESFFLGMANLSENYSEFVQTRVI 113
----HHHHHHHHHHHHHHHHHHHHHHHH----EEEEEE
98 residues (89.09%) 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: 18.63% helical, 40.20% extended, 41.18% loops/other (query: 24.55% 33.64% 41.82%)
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.55.1.2.1_A b.55.1.2 99.36.35.5 GUESS -28.345 0 1 90.00% 16.16% OPTM -265.764 -148.090 1.222 0.438 0.276 0.731 0.757 10.050 -24.7 1.960 0.000 -29.0 1.590 -5.000 -60.5 -0.370 0.960 -0.2 0.910 0.360 -15.4 -0.040 -4.270 9.2 1.160 0.220 -12.3 2.050 9.850 -10.6 10.460 11.310 -36.6 -30.000 37.000 -57.0 -30.000 14.000 -67.0 2.960 41.500 -5.5 2.030 9.000 -42.0 1.750 -1.000 -24.0 4.690 11.000 -53.0 5.000 -2.2 -2.876 -63.8 21.000 116.0 5.000 -2.2 0.491 0.0 0.78 0.75
alignment source: OPTM
---EEEEE-- ----EEEEEE--- -EEEEE------HHHHHHHHHHHHH-- --- --EEEEE-----
Query: 1 MSGWYELSKS-SNDQFKFVLKAGN-----GEVILTSELYTGKSGAMNGIESVQTNS-------PIE--ARYAKEVAKNDK 65
Sbjct: 13 VRKVGYLRKPKSMHKRFFVLRAASEAGGPARLEYYEN-----------EKKWRHKSSAPKRSIPLESCFNINKRADSKNK 81
EEEEEEE------EEEEEEE---------EEEEE--H HHHH-------EEEE---EEEEEEE-------
EEEEEEE---EEEEE-----HHHHHHHHHHHHHH
Query: 66 PYFNLKAANHQIIGTSQMYSSTAARDNGIKSVME 99
Sbjct: 82 HLVALYTRDEHFAIAAD---SEAEQDSWYQALLQ 112
EEEEEE---EEEEE--- HHHHHHHHHHHHHH
99 residues (90.00%) of query sequence aligned
DONE: Mon Jun 30 20:46:38 2008 EST