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:Thu Aug 14 17:34:07 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 T0432
--> 130 residues, sequence name: T0432
Database: T:\CBSU\blastdb\20080108\nr
PDB structure 2DKW with significant sequence identity (69.35%) has been detected:
pdb|2DKW|A Chain A, Solution Structure Of The Bromodomain Of Human Protein Kiaa1240
This structure may be a good candidate for homology modeling procedure
sequence_identity= 86/124 (69.35%) (length difference of 4.62%)
Query: 6 DTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKY 65
+T RELR+FLR+VT RLA DKRF +F+KPV DY+ VIK+PMDLS+VI+KID H Y
Sbjct: 8 NTLRELRLFLRDVTKRLATDKRFNIFSKPVS-----DYLEVIKEPMDLSTVITKIDKHNY 62
Query: 66 LTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEE 125
LT KD+L+DIDLICSNALEYNPD+DPGD++IRHRAC L+DTA+AII ELD +F +LCEE
Sbjct: 63 LTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEE 122
Query: 126 IQES 129
I+ES
Sbjct: 123 IKES 126
-> 26 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 | 58 | 2 | 0 | 9 | 15 | 1 | 16 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 2.90 | 3.39 | 3.87 | 3.58 |
2 | 2.90 | 0.00 | 2.03 | 2.18 | 2.54 |
3 | 3.39 | 2.03 | 0.00 | 2.50 | 1.85 |
4 | 3.87 | 2.18 | 2.50 | 0.00 | 2.78 |
5 | 3.58 | 2.54 | 1.85 | 2.78 | 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 | 100.00 | 73.83 | 68.97 | 76.42 |
2 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
3 | 73.83 | 100.00 | 100.00 | 100.00 | 100.00 |
4 | 68.97 | 100.00 | 100.00 | 100.00 | 100.00 |
5 | 76.42 | 100.00 | 100.00 | 100.00 | 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 | 100.00 | 100.00 | 100.00 |
2 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
3 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
4 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
5 | 100.00 | 100.00 | 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: 58.27% helical, 0.00% extended, 41.73% loops/other (query: 70.00% 1.54% 28.46%)
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.
2DKW_A not_found 75.75.75.75 NONE -31.732 0 1 95.38% 67.44% OPTM -430.979 -329.480 7.865 0.621 0.897 0.927 0.941 49.950 -74.8 30.490 472.500 -566.0 43.550 465.000 -591.0 2.880 4.070 -26.1 3.720 6.070 -31.4 21.500 72.950 -89.6 37.550 76.300 -99.5 19.050 56.220 -92.5 28.360 55.320 -100.0 -30.000 31.000 -100.0 -30.000 30.000 -106.0 28.860 406.000 -432.0 47.180 384.000 -452.0 8.430 49.000 -83.0 12.930 49.000 -101.0 5.000 -48.5 -18.477 -15.6 0.000 -9.3e+061 5.000 -48.5 -3.000 -50.2 0.85 0.73
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HHHHHHHHHHHHHHHHHHHHHH-----EE---- -------HHHHHH----HHHHHHHHH------HHHHHHHHHHHH
Query: 1 SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPV-DPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLIC 79
Sbjct: 3 SGSSGNTLRELRLFLRDVTKRLATDKRFNIFSKPVSDYLEV------IKEPMDLSTVITKIDKHNYLTAKDFLKDIDLIC 76
----HHHHHHHHHHHHHHHHHHH------------------ -----HHHHHHHHH-------HHHHHHHHHHHH
HHHHHH-------HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Query: 80 SNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQES 129
Sbjct: 77 SNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIKES 126
HHHH--------HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHH---
124 residues (95.38%) 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: 57.55% helical, 0.00% extended, 42.45% loops/other (query: 70.00% 1.54% 28.46%)
SCOP classification: [All alpha proteins]/[Bromodomain-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.
1E6I_A a.29.2.1 127.6.5.5 NONE -32.015 0 1 77.69% 28.57% OPTM -274.587 -268.340 3.985 0.704 0.702 0.910 0.953 23.270 -42.4 7.040 109.000 -125.0 9.660 115.000 -175.0 4.310 10.320 -15.7 4.520 10.050 -35.1 10.480 25.180 -21.5 14.370 28.410 -48.1 14.210 30.340 -47.1 18.320 30.420 -69.3 -30.000 23.000 -77.0 -30.000 26.000 -93.0 11.780 168.000 -167.0 23.510 176.000 -218.0 6.270 35.000 -49.0 11.290 34.000 -90.0 5.000 -27.7 -1.219 -30.4 0.000 -9.3e+061 5.000 -27.7 -0.229 -12.7 0.51 0.72
alignment source: OPTM
HHHHHHHHHHHHH-----EE-----------HHHHHH----HHHHHHHHH------HHHHHHHHHHHHHHHHHH------
Query: 12 RIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDP 91
Sbjct: 333 DAAIQNILTELQNHAAAWPFLQPVNKEEVPDYYDFIKEPMDLSTMEIKLESNKYQKMEDFIYDARLVFNNCRMYNGENT- 411
HHHHHHHHHHHH------------------HHHH------HHHHHHHHH------HHHHHHHHHHHHHHHHHH-----H
-HHHHHHHHHHHHHHHHHHHHHH--
Query: 92 GDRLIRHRACALRDTAYAIIKEELD 116
Sbjct: 412 ---SYYKYANRLEKFFNNKVKEIPE 433
HHHHHHHHHHHHHHHHH-----
101 residues (77.69%) 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: 58.56% helical, 0.00% extended, 41.44% loops/other (query: 70.00% 1.54% 28.46%)
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.
2E7O_A not_found 75.75.75.75 NONE -32.300 0 1 79.23% 20.56% OPTM -434.249 -224.220 3.714 0.671 0.830 0.905 0.947 19.530 -37.1 4.460 62.000 -92.5 7.690 69.500 -147.5 1.230 1.060 -8.9 3.140 6.410 -35.2 4.850 15.040 -10.3 10.490 20.570 -43.8 7.880 20.300 -39.6 14.160 23.920 -61.5 -30.000 10.000 -73.0 -30.000 19.000 -87.0 11.090 153.000 -160.0 22.440 157.000 -198.0 7.080 14.000 -51.0 11.270 39.000 -94.0 5.000 -23.7 -3.929 -40.8 0.000 -9.3e+061 5.000 -23.7 5.000 -8.4 0.61 0.74
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHHHH-----EE-----------HHHHHH----HHHHHHHHH------HHHHHHHHHHHHHHHHHH----
Query: 10 ELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR 89
Sbjct: 10 KDLALCSMILTEMETHEDAWPFLLPVNLKLVPGYKKVIKKPMDFSTIREKLSSGQYPNLETFALDVRLVFDNCETFNEDD 89
HHHHHHHHHHHHH-----HHHH--------------------HHHHHHHHHH-----HHHHHHHHHHHHHHHHHH-----
---HHHHHHHHHHHHHHHHHHHHHH--
Query: 90 DPGDRLIRHRACALRDTAYAIIKEELD 116
Sbjct: 90 SD----IGRAGHNMRKYFEKKWTDTFK 112
HH HHHHHHHHHHHHHHHHHH--K
103 residues (79.23%) 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: 63.16% helical, 0.00% extended, 36.84% loops/other (query: 70.00% 1.54% 28.46%)
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.
2D9E_A not_found 75.75.75.75 NONE -32.395 0 1 82.31% 28.45% OPTM -385.049 -266.930 4.805 0.630 0.774 0.874 0.912 26.410 -47.0 9.040 179.000 -198.0 16.180 144.000 -218.5 3.050 6.370 -24.0 2.590 6.960 -31.5 8.050 24.840 -33.7 14.320 30.440 -48.2 11.940 28.810 -62.4 17.040 31.600 -71.6 -30.000 28.000 -97.0 -30.000 26.000 -99.0 18.410 280.000 -288.0 30.280 269.000 -306.0 5.950 17.000 -60.0 9.180 17.000 -84.0 5.000 -34.5 -3.370 -35.1 0.000 -9.3e+061 5.000 -34.5 0.279 -14.5 0.59 0.83
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHHHH-----EE-----------HHHHHH----HHHHHHHHH------HHHHHHHHHHHHHHHHHH----
Query: 10 ELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDR 89
Sbjct: 7 GFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKD 86
HHHHHHHHHHHHHHH-----------------HHHH------HHHHHHHHH------HHHHHHHHHHHHHHHHHH-----
---HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Query: 90 DPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEE 125
Sbjct: 87 T----IFYRAAVRLREQGGAVLRQ-----ARRQAEK 113
H HHHHHHHHHHHHHHHHHHH HHHHHH-
107 residues (82.31%) 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: 55.75% helical, 0.00% extended, 44.25% loops/other (query: 70.00% 1.54% 28.46%)
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.
2RNW_A not_found 75.75.75.75 NONE -32.428 0 1 78.46% 25.47% OPTM -362.002 -322.040 3.469 0.593 0.835 0.857 0.953 18.720 -40.0 5.560 93.500 -113.5 9.520 78.500 -160.5 0.470 4.090 -13.9 0.520 -1.070 -46.3 0.490 9.250 1.8 5.690 17.850 -52.7 2.030 7.990 -29.2 11.880 25.130 -70.7 -30.000 6.000 -75.0 -30.000 21.000 -92.0 10.740 171.000 -159.0 21.280 160.000 -197.0 7.090 32.000 -78.0 10.610 41.000 -112.0 5.000 -24.4 5.546 -40.2 0.000 -9.3e+061 5.000 -24.4 -1.721 -9.5 0.63 0.68
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHHHHHHHHHHHHH-----EE-----------HHHHHH----HHHHHHHHH------HHHHHHHHHHHHHHHHHH--
Query: 8 FRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNP 87
Sbjct: 725 PDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNP 804
HHHHHHHHHHHHHHHH----HHHH--------------------HHHHHHHHH------HHHHHHHHHHHHHHHHH----
-----HHHHHHHHHHHHHHHHHHHHH
Query: 88 DRDPGDRLIRHRACALRDTAYAIIKE 113
Sbjct: 805 PESEY----YKCANILEKFFFSKIKE 826
----H HHHHHHHHHHHHHHHH-
102 residues (78.46%) of query sequence aligned
DONE: Thu Aug 14 21:45:29 2008 EST