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 05:29:08 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 T0408
--> 104 residues, sequence name: T0408
Database: T:\CBSU\blastdb\20080108\nr
-> 11 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 | 3 | 21 | 2 | 1 | 2 | 6 | 0 | 1 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 4.44 | 8.67 | 8.67 | 8.16 |
2 | 4.44 | 0.00 | 7.97 | 7.57 | 7.13 |
3 | 8.67 | 7.97 | 0.00 | 3.36 | 3.34 |
4 | 8.67 | 7.57 | 3.36 | 0.00 | 3.67 |
5 | 8.16 | 7.13 | 3.34 | 3.67 | 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 | 55.70 | 40.00 | 38.03 | 35.90 |
2 | 55.70 | 100.00 | 55.56 | 63.89 | 47.44 |
3 | 40.00 | 55.56 | 100.00 | 66.20 | 95.65 |
4 | 38.03 | 63.89 | 66.20 | 100.00 | 55.71 |
5 | 35.90 | 47.44 | 95.65 | 55.71 | 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 | 100.00 | 71.43 | 84.51 | 73.08 |
2 | 100.00 | 100.00 | 72.22 | 84.72 | 78.21 |
3 | 71.43 | 72.22 | 100.00 | 100.00 | 100.00 |
4 | 84.51 | 84.72 | 100.00 | 100.00 | 100.00 |
5 | 73.08 | 78.21 | 100.00 | 100.00 | 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: 65.91% helical, 0.00% extended, 34.09% loops/other (query: 77.88% 0.00% 22.12%)
SCOP classification: [All alpha proteins]/[Cyclin-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.
a.74.1.2.1_A a.74.1.2 127.5.5.1 GUESS -25.791 0 1 75.96% 16.46% OPTM -351.081 -201.790 1.133 0.626 0.596 0.809 0.968 6.410 -25.0 2.440 43.000 -47.5 3.850 36.500 -86.0 -0.810 -2.390 -0.9 -0.450 0.930 -27.9 -0.610 -1.340 10.2 1.650 5.420 -27.5 0.170 -4.190 -20.1 6.370 9.050 -46.2 -30.000 -8.000 -59.0 -30.000 -2.000 -69.0 0.880 11.000 -2.0 -0.190 -6.000 -36.0 0.900 0.000 -19.0 2.860 4.000 -56.0 5.000 -1.3 6.069 -67.0 21.000 195.0 5.000 -1.3 5.000 5.0 0.51 0.76
alignment source: OPTM
HHHHHHHHH-- HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH----HHHHHHHHHH
Query: 8 GEGMKVVKEKY---PDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRV 84
Sbjct: 118 FKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVSRISKKEIGRCFKL 197
HHHHHHHHH----HHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHH------HHHHH------HHHHHHHHHHH
HH
Query: 85 VL 86
Sbjct: 198 IL 199
HH
79 residues (75.96%) 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: 74.47% helical, 0.00% extended, 25.53% loops/other (query: 77.88% 0.00% 22.12%)
SCOP classification: [All alpha proteins]/[Cyclin-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.
a.74.1.1.6_B a.74.1.1 127.5.5.4 GUESS -26.146 0 1 77.88% 18.52% OPTM -413.769 -225.420 1.532 0.679 0.377 0.737 0.954 2.900 -24.5 2.180 7.000 -47.5 2.080 13.500 -70.5 1.770 7.000 -19.2 2.060 4.810 -27.8 2.910 9.140 -13.4 3.850 9.090 -27.1 1.770 5.870 -38.2 3.560 5.750 -44.9 -30.000 2.000 -74.0 -30.000 -2.000 -76.0 2.880 18.000 -26.0 2.950 13.000 -52.0 2.260 9.000 -8.0 4.070 7.000 -45.0 5.000 -2.0 -0.268 -47.2 0.000 -9.3e+061 5.000 -2.0 5.000 -1.7 0.65 0.93
alignment source: OPTM
HHHHHHH HH--HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHH--H HHHHHHHHHHHHH----HHHHHHHH
Query: 8 GEGMKVV---KEKYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDE--VAIEKQMKSAMKELGITKEEIADVL 82
Sbjct: 154 CYILHIMHAPREDYLNIYNLCRPKIFCALCDGRSAMKRPVLITLACMHLTMNQKYDYYENRIDGVCKSLYITKEELHQCC 233
HHHHH----HHHHHHHHHHHHHHHHHHHH-HHHH---HHHHHHHHHHHHH----HHHHHHHHHHHHH----HHHHHHHHH
HHHHHH
Query: 83 RVVLLT 88
Sbjct: 234 DLVDIA 239
HHHHHH
81 residues (77.88%) 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: 73.40% helical, 0.00% extended, 26.60% loops/other (query: 77.88% 0.00% 22.12%)
SCOP classification: [All alpha proteins]/[AhpD-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.
1VKE_A a.152.1.2 127.5.5.3 GUESS -26.670 0 1 84.62% 23.86% OPTM -379.209 -230.640 2.030 0.695 0.298 0.760 0.897 10.390 -26.4 4.030 47.000 -81.0 10.300 89.000 -147.0 -0.830 0.780 -10.4 1.490 3.660 -22.1 -0.490 -0.680 0.1 0.790 -0.720 -14.7 0.330 2.140 -32.4 5.960 5.430 -46.3 -30.000 3.000 -75.0 -30.000 2.000 -80.0 5.230 79.000 -85.0 17.180 124.000 -163.0 -0.320 6.000 14.0 -0.660 -8.000 -32.0 5.000 -12.2 -1.991 -37.9 0.000 -9.3e+061 5.000 -12.2 5.000 5.0 0.78 0.91
alignment source: OPTM
--HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH----HHHHHHHHHHHHHH-- HHH
Query: 17 KYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLLTSG---MPA 93
Sbjct: 19 RGTLNTKRFFNLDSAVYRPGKLDVKTKELMGLVASTVLRCDDCIRYHLVRCVQE-GASDEEIFEALDIALVVGGSIVIPH 97
--HHHHHHHHHHHH--------HHHHHHHHHHHHHH---HHHHHHHHHHHHH-- --HHHHHHHHHHHHHHH----HHHH
HHHHHHHHHHH
Query: 94 FTKAMKILEKL 104
Sbjct: 98 LRRAVGFLEEL 108
HHHHHHHHHHH
88 residues (84.62%) 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: 73.33% helical, 0.00% extended, 26.67% loops/other (query: 77.88% 0.00% 22.12%)
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.
3BEY_A not_found 124.124.124.124 GUESS -26.752 0 1 68.27% 20.83% OPTM -263.292 -124.210 2.069 0.581 0.341 0.707 0.847 9.540 -21.3 6.600 96.000 -107.5 7.810 81.000 -128.0 -0.120 -0.860 4.5 -0.190 -0.370 -13.0 2.480 6.220 4.0 1.130 1.230 -12.3 4.950 7.180 -24.5 5.970 5.970 -39.3 -30.000 0.000 -61.0 -30.000 4.000 -70.0 10.060 137.000 -127.0 15.430 118.000 -162.0 -1.020 -1.000 78.0 2.980 -1.000 -23.0 5.000 -10.0 -4.580 -41.0 0.000 -9.3e+061 5.000 -10.0 0.279 -4.2 0.68 0.91
alignment source: OPTM
H--HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH----HHHHHHHHHHHHH
Query: 16 EKYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLL 87
Sbjct: 10 EELPEVAESFKNFREAVRSEGKLT-EREKLLISVACSVAVRCDACTRRHAEEALEAGITEGELAEAAAVAAL 80
--HHHHHHHHHHHHHHH------H HHHHHHHHHHHHH---HHHHHHHHHHHH-----HHHHHHHHHHHHHH
71 residues (68.27%) 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: 56.73% helical, 0.00% extended, 43.27% loops/other (query: 77.88% 0.00% 22.12%)
SCOP classification: [All alpha proteins]/[AhpD-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.
2CWQ_A a.152.1.4 127.5.5.1 GUESS -26.927 0 1 81.73% 22.35% OPTM -257.903 -82.070 1.967 0.548 0.197 0.757 0.925 12.000 -24.0 6.250 94.000 -125.0 5.790 61.500 -127.5 1.270 2.960 -13.5 0.460 1.200 -15.7 3.160 9.340 -10.9 2.190 4.790 -14.4 6.190 16.570 -45.9 8.110 8.820 -48.4 -30.000 17.000 -83.0 -30.000 11.000 -86.0 7.040 81.000 -94.0 7.630 50.000 -99.0 2.720 6.000 51.0 4.230 9.000 -26.0 5.000 -10.3 -0.276 -50.4 0.000 -9.3e+061 5.000 -10.3 -1.387 -5.7 0.89 0.58
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
------ -HHHHHHHHH--HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH----HHHH
Query: 1 MKNEVF--FGEGMKVVKEKYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEI 78
Sbjct: 29 AAENLGEGLPRAIPLLAEKAPGLLLEHGRSWTYAPEKGALDEKTRTLILLGIALATGSEACVKAA--HRAKRLGLSKEAL 106
----------HHHHHHHH-HHHHHHHHHHHHH--------HHHHHHHHHHHHHHH--HHHHH--H HHHHH---HHHHH
HHHHHHH
Query: 79 ADVLRVV 85
Sbjct: 107 LETLKIA 113
HHHHHHH
85 residues (81.73%) of query sequence aligned
DONE: Sun Aug 10 08:25:15 2008 EST