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 19:25:04 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 T0444
--> 326 residues, sequence name: T0444
Database: T:\CBSU\blastdb\20080108\nr
PDB structure 2UW2 with significant sequence identity (84.59%) has been detected:
pdb|2UW2|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase Subunit R2
This structure may be a good candidate for homology modeling procedure
sequence_identity= 247/292 (84.59%) (length difference of 10.43%)
Query: 35 EEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFIS 94
+EPLLR++ RRFVIFPI+Y DIW+MYK+A+ASFWTAEEVDLSKD+ HW LK +E+YFIS
Sbjct: 12 DEPLLRENPRRFVIFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWESLKPEERYFIS 71
Query: 95 HILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPK 154
H+LAFFAASDGIVNENLVERFSQEVQ+ EARCFYGFQI +EN+HSEMYSLLIDTYI+DPK
Sbjct: 72 HVLAFFAASDGIVNENLVERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPK 131
Query: 155 KREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKK 214
+REFLFNAIETMP VKKKADWALRWI D+++T+GERVVAFAAVEG+FFSGSFA+IFWLKK
Sbjct: 132 EREFLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKK 191
Query: 215 RGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEAL 274
RG MPGLTFSNELISRDEGLHCDFACLMF++LV+KPSEERVREII++AV+IEQEFLTEAL
Sbjct: 192 RGPMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLTEAL 251
Query: 275 PVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMENISLEGKTN 326
PV LIGMNC LMKQYIEFVADRL++ELGFSKVF+ ENPFDFMENISLEGKTN
Sbjct: 252 PVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFMENISLEGKTN 303
PDB structure 1H0N with significant sequence identity (80.72%) has been detected:
ref|NP_033130.1| ribonucleotide reductase M2 [Mus musculus] sp|P11157|RIR2_MOUSE Ribonucleoside-diphosphate reductase subunit M2 (Ribonucleotide reductase small subunit) (Ribonucleotide reductase small chain) pdb|1H0N|A Chain A, Cobalt Substitution Of Mouse R2 Ribonucleotide Reductase To Model The Reactive Diferrous State pdb|1H0O|A Chain A, Cobalt Substitution Of Mouse R2 Ribonucleotide Reductase To Model The Reactive Diferrous State pdb|1W68|A Chain A, Crystal Structure Of Mouse Ribonucleotide Reductase Subunit R2 Under Oxidizing Conditions. A Fully Occupied Dinuclear Iron Cluster. pdb|1W69|A Chain A, Crystal Structure Of Mouse Ribonucleotide Reductase Subunit R2 Under Reducing Conditions. A Fully Occupied Dinuclear Iron Cluster And Bound Acetate. pdb|1XSM|A Chain A, Protein R2 Of Ribonucleotide Reductase From Mouse emb|CAA33707.1| M2 ribonucleotide reductase [Mus musculus] gb|AAA40062.1| ribonucleotide reductase subunit M2 dbj|BAC40647.1| unnamed protein product [Mus musculus]
This structure may be a good candidate for homology modeling procedure
sequence_identity= 247/306 (80.72%) (length difference of 6.13%)
Query: 21 QSMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLP 80
+S + TN S +EPLLR++ RRFV+FPI+Y DIW+MYK+A+ASFWTAEEVDLSKD+
Sbjct: 59 ESKAPTNPSV---EDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQ 115
Query: 81 HWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSE 140
HW LK DE++FISH+LAFFAASDGIVNENLVERFSQEVQV EARCFYGFQI +EN+HSE
Sbjct: 116 HWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSE 175
Query: 141 MYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGV 200
MYSLLIDTYI+DPK+RE+LFNAIETMP VKKKADWALRWI D+++T+GERVVAFAAVEG+
Sbjct: 176 MYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGI 235
Query: 201 FFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIV 260
FFSGSFA+IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMF++LV+KP+E+RVREII
Sbjct: 236 FFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIIT 295
Query: 261 DAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMENIS 320
+AV+IEQEFLTEALPV LIGMNC LMKQYIEFVADRL++ELGF+K+F+ ENPFDFMENIS
Sbjct: 296 NAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENPFDFMENIS 355
Query: 321 LEGKTN 326
LEGKTN
Sbjct: 356 LEGKTN 361
PDB structure 1JK0 with significant sequence identity (68.60%) has been detected:
pdb|1JK0|A Chain A, Ribonucleotide Reductase Y2y4 Heterodimer
This structure may be a good candidate for homology modeling procedure
sequence_identity= 201/293 (68.60%) (length difference of 10.12%)
Query: 35 EEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN-KLKADEKYFI 93
EEPLL + R V+FPI+Y +IW+ YK+A+ASFWTAEE+DLSKD+ WN ++ +E++FI
Sbjct: 95 EEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFI 154
Query: 94 SHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDP 153
S +LAFFAASDGIVNENLVE FS EVQ+PEA+ FYGFQI+IEN+HSE YSLLIDTYI+DP
Sbjct: 155 SRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDP 214
Query: 154 KKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLK 213
K+ EFLFNAI T+P + +KA+WALRWI D + FGER+VAFA++EGVFFSGSFA+IFWLK
Sbjct: 215 KESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLK 274
Query: 214 KRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEA 273
KRG+MPGLTFSNELI RDEGLH DFACL+F +L NKP V +I+ +AV+IEQ + +A
Sbjct: 275 KRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDA 334
Query: 274 LPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMENISLEGKTN 326
LPV L+GMN LM QY+EFVADRLLV G K ++ ENPFDFMENISL GKTN
Sbjct: 335 LPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMENISLAGKTN 387
PDB structure 1SMQ with significant sequence identity (68.60%) has been detected:
ref|NP_012508.1| Ribonucleotide-diphosphate reductase (RNR), small subunit; the RNR complex catalyzes the rate-limiting step in dNTP synthesis and is regulated by DNA replication and DNA damage checkpoint pathways via localization of the small subunits [Saccharomyces cerevisiae] sp|P09938|RIR2_YEAST Ribonucleoside-diphosphate reductase small chain 1 (Ribonucleotide reductase small subunit 1) (Ribonucleotide reductase R2 subunit 1) pdb|1SMQ|A Chain A, Structure Of The Ribonucleotide Reductase Rnr2 Homodimer From Saccharomyces Cerevisiae pdb|1SMQ|B Chain B, Structure Of The Ribonucleotide Reductase Rnr2 Homodimer From Saccharomyces Cerevisiae pdb|1SMQ|C Chain C, Structure Of The Ribonucleotide Reductase Rnr2 Homodimer From Saccharomyces Cerevisiae pdb|1SMQ|D Chain D, Structure Of The Ribonucleotide Reductase Rnr2 Homodimer From Saccharomyces Cerevisiae gb|AAA34988.1| ribonucleoside diphosphate reductase small subunit emb|CAA89317.1| RNR2 [Saccharomyces cerevisiae]
This structure may be a good candidate for homology modeling procedure
sequence_identity= 201/293 (68.60%) (length difference of 10.12%)
Query: 35 EEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN-KLKADEKYFI 93
EEPLL + R V+FPI+Y +IW+ YK+A+ASFWTAEE+DLSKD+ WN ++ +E++FI
Sbjct: 75 EEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERFFI 134
Query: 94 SHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDP 153
S +LAFFAASDGIVNENLVE FS EVQ+PEA+ FYGFQI+IEN+HSE YSLLIDTYI+DP
Sbjct: 135 SRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDP 194
Query: 154 KKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLK 213
K+ EFLFNAI T+P + +KA+WALRWI D + FGER+VAFA++EGVFFSGSFA+IFWLK
Sbjct: 195 KESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLK 254
Query: 214 KRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEA 273
KRG+MPGLTFSNELI RDEGLH DFACL+F +L NKP V +I+ +AV+IEQ + +A
Sbjct: 255 KRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDA 314
Query: 274 LPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMENISLEGKTN 326
LPV L+GMN LM QY+EFVADRLLV G K ++ ENPFDFMENISL GKTN
Sbjct: 315 LPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMENISLAGKTN 367
-> 191 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 | 0 | 0 | 0 | 27 | 83 | 81 | 28 | 19 |
1 | 2 | 3 | 4 | 5 | |
1 | 0.00 | 1.84 | 1.93 | 2.48 | 1.87 |
2 | 1.84 | 0.00 | 1.83 | 2.55 | 2.08 |
3 | 1.93 | 1.83 | 0.00 | 2.01 | 1.28 |
4 | 2.48 | 2.55 | 2.01 | 0.00 | 3.86 |
5 | 1.87 | 2.08 | 1.28 | 3.86 | 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 | 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 | 96.03 |
5 | 100.00 | 100.00 | 100.00 | 96.03 | 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: 63.14% helical, 0.00% extended, 36.86% loops/other (query: 66.26% 1.53% 32.21%)
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.
2UW2_A not_found 100.100.100.100 NONE -84.305 0 1 84.36% 79.30% OPTM -1749.207 -1029.810 16.566 0.686 0.956 0.964 0.999 131.270 -175.4 51.960 1443.500 -1400.0 85.520 1408.500 -1550.0 1.290 14.330 -6.1 6.680 25.230 -92.3 25.610 188.510 -137.3 63.660 224.150 -268.3 24.450 114.460 -159.3 50.130 135.700 -242.3 -30.000 17.000 -193.0 -30.000 25.000 -231.0 46.710 1105.000 -1039.0 114.010 1113.000 -1194.0 7.490 63.000 -142.0 17.040 88.000 -260.0 5.000 -1.0 -7.742 -6.5 0.000 -9.3e+061 5.000 -1.0 -0.347 -1.0 0.68 0.91
alignment source: OPTM
-------------EEEEE----HHHHHHHHHHHH----------HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Query: 32 KSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENL 111
Sbjct: 66 GVEDEPLLRENP----IFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWESLKPEERYFISHVLAFFAASDGIVNENL 141
------------ ------HHHHHHHHHHHH-------------HHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHH
Query: 112 VERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERV 191
Sbjct: 142 VERFSQEVQITEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREFLM------PCVKKKADWALRWIGDKEATYGERV 215
HH-HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH---- ---------HHHHHH-----HHHHH
HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH--HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Query: 192 VAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLT 271
Sbjct: 216 VAFAAVEGIFFSGSFASIFWLKKRGPMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPSEERVREIIINAVRIEQEFLT 295
HHHHHHHH---HHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
HH---------HHHHHHHHHHHHHHHHHH--------------HH
Query: 272 EALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFM 316
Sbjct: 296 EALPVKLIGMNCTLMKQYIEFVADRLMLELGFSKVFRVENPFDFM 340
-----------HHHHHHHHHHHHHHHHHH----------------
275 residues (84.36%) 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: 65.85% helical, 0.00% extended, 34.15% loops/other (query: 66.26% 1.53% 32.21%)
SCOP classification: [All alpha proteins]/[Ferritin-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.
1H0N_A a.25.1.2 183.30.30.19 NONE -84.542 0 1 88.34% 81.25% OPTM -1750.718 -1046.850 18.284 0.702 0.967 0.999 0.999 134.270 -187.5 56.260 1532.500 -1527.0 89.470 1503.000 -1653.5 3.150 16.680 -34.3 8.380 37.590 -107.9 28.450 199.510 -181.8 55.850 247.760 -294.1 33.370 126.410 -197.6 54.630 159.790 -271.4 -30.000 21.000 -227.0 -30.000 33.000 -257.0 55.120 1251.000 -1191.0 129.010 1224.000 -1312.0 8.670 81.000 -195.0 20.950 110.000 -288.0 5.000 -1.0 -8.966 -4.7 0.000 -9.3e+061 5.000 -1.0 -0.770 -1.0 0.68 0.96
alignment source: OPTM
---------------EEEEE----HHHHHHHHHHHH----------HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
Query: 30 EIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNE 109
Sbjct: 65 NPSVEDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNE 144
------------------------HHHHHHHHHHHH------------HHHHHHH--HHHHHHHHHHHHHH--HHHHHHH
HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHH
Query: 110 NLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGE 189
Sbjct: 145 NLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGE 224
HHH--HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH------HHHHHHHHHHHHHHH-----HHH
HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH--HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Query: 190 RVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEF 269
Sbjct: 225 RVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEF 304
HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHH
HHHH---------HHHHHHHHHHHHHHHHHH--------------HHH
Query: 270 LTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFME 317
Sbjct: 305 LTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENPFDFME 352
HH-----------HHHHHHHHHHHHHHHHHH-----------------
288 residues (88.34%) 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: 64.98% helical, 0.00% extended, 35.02% loops/other (query: 66.26% 1.53% 32.21%)
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.
2P1I_A not_found 100.100.100.100 NONE -84.601 0 1 78.83% 59.70% OPTM -1585.721 -816.340 13.850 0.685 0.925 0.976 0.995 90.810 -134.8 37.950 839.500 -810.5 55.350 876.500 -1040.5 2.780 19.700 0.5 4.870 15.020 -75.6 17.350 96.220 -39.8 45.160 143.830 -184.1 19.670 63.290 -88.0 34.370 98.200 -196.6 -30.000 11.000 -161.0 -30.000 30.000 -215.0 46.380 981.000 -893.0 109.570 996.000 -1095.0 2.960 44.000 -46.0 14.240 75.000 -210.0 5.000 -1.0 -2.504 -8.6 0.000 -9.3e+061 5.000 -1.0 -0.481 -82.0 0.53 0.94
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
--HHHHHHHHHHHH----------HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH
Query: 52 QYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQ 131
Sbjct: 47 MYPEVWNFYKKAEASFWTAEEIDLSSDLKDFEKLNVNEKHFIKHVLAFFAAS-----ENLASKFLREVEIIEAKKFYSFQ 121
--HHHHHHHHHHH---------------HHHHH-----HHHHHHHHHHH--- ---HHHHHHH---HHHHHHHHHH
HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Query: 132 ILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFW 211
Sbjct: 122 IAVENIHSETYSLLIDNYIKDEKERLNLFHAIENIPAIKNKALWAAKWINDTNS-FAERIVANACVEGILFSGSFCAIFW 200
HHHHHHHHHHHHHHHHHH---HHHHHH--HHHH--HHHHHHHHHHHH------- HHHHHHHHHHH-----HHHHHHHHH
HHH----HHHHHHHHHHHH--HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Query: 212 LKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIE 291
Sbjct: 201 FKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPENVVQNIVKEAVEVERSFICESLPCDLIGMNSRLMSQYIE 280
HH-------HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH------------HHHHHHHHH
HHHHHHHHH--------------
Query: 292 FVADRLLVELGFSKVFQAENPFD 314
Sbjct: 281 FVADRLLECLGCSKVFHSKNPFN 303
HHHHHHHHH--------------
257 residues (78.83%) 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: 64.81% helical, 0.00% extended, 35.19% loops/other (query: 66.26% 1.53% 32.21%)
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.
2O1Z_A not_found 100.100.100.100 NONE -85.159 0 1 87.12% 54.30% OPTM -1680.771 -916.340 15.158 0.577 0.830 0.938 0.983 98.550 -147.3 39.240 1001.000 -1004.5 61.170 943.000 -1108.5 3.640 18.950 -38.6 6.930 21.000 -89.7 20.490 152.310 -126.9 43.050 147.960 -199.2 23.150 96.140 -165.2 37.330 110.190 -217.7 -30.000 34.000 -228.0 -30.000 31.000 -245.0 48.400 1107.000 -1060.0 118.010 1062.000 -1155.0 7.180 83.000 -178.0 12.330 57.000 -238.0 5.000 -1.0 -2.838 -8.9 0.000 -9.3e+061 5.000 -1.0 -0.432 -86.5 0.57 0.94
alignment source: OPTM
+++ there is a problem with all-atom model, click here for details
HHHHHH------------------------EEEEE----HHHHHHHHHHHH----------HHHHHHHHH--HHHHHHHH
Query: 15 TENLYFQSMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFIS 94
Sbjct: 19 FSDLQKSK----------EANEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEKLNDNEKHFIK 88
HHHHH--- --------------------HHHHHHHHHHHH----------HHHHHHHHH--HHHHHHHHH
HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Query: 95 HILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKAD 174
Sbjct: 89 HVLAFFAAS-------LASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAIENIPAVKNKAL 161
HHHHHHH-- HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH---HHHHHHHHH
HHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH--HHHHHHHHHHHHHHH----HHH
Query: 175 WALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEER 254
Sbjct: 162 WAAKWIND-TNSFAERIVANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEV 240
HHHH---- --HHHHHHHHHHHHH---HHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHH
HHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHH--------------HH
Query: 255 VREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFM 316
Sbjct: 241 VQNIVKEAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFHAKNPFNWM 302
HHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHH-----------------
284 residues (87.12%) 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: 57.98% helical, 0.00% extended, 42.02% loops/other (query: 66.26% 1.53% 32.21%)
SCOP classification: [All alpha proteins]/[Ferritin-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.
1JK0_A a.25.1.2 183.30.30.19 NONE -85.195 0 1 93.25% 64.80% OPTM -1666.733 -1046.300 16.638 0.652 0.930 0.926 0.995 112.820 -159.8 45.950 1313.000 -1351.5 83.130 1245.500 -1382.5 3.720 31.180 -72.3 3.140 12.710 -85.0 31.360 217.220 -219.0 46.460 194.550 -237.3 25.250 124.170 -224.9 35.490 134.290 -239.9 -30.000 35.000 -248.0 -30.000 36.000 -254.0 54.610 1282.000 -1249.0 111.050 1201.000 -1288.0 9.260 113.000 -242.0 14.790 83.000 -268.0 5.000 -1.0 -5.530 -5.6 0.000 -9.3e+061 5.000 -1.0 -0.620 -1.0 0.53 0.80
alignment source: OPTM
HHHHHH------------ ------------EEEEE----HHHHHHHHHHHH----------HHHHHHHHH --HHHHH
Query: 15 TENLYFQSMSDTNESEIK--SNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNK-LKADEKY 91
Sbjct: 54 NHKAYLKSH-QVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNNRMNENERF 132
HHHHHHH-H HHHHHHHHH---------------------HHHHHHHHHHH-------------HHHHHHH---HHHHHH
HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Query: 92 FISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKK 171
Sbjct: 133 FISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGE 212
HHHHHHHHH----HHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH---HHHHHH
HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH--HHHHHHHHHHHHHHH----
Query: 172 KADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 251
Sbjct: 213 KAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPD 292
HHHHHHH-------HHHHHHHHHHHHH---HHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH-------H
HHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHH--------------HHHH
Query: 252 EERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMEN 318
Sbjct: 293 PAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFMEN 359
HHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHH-------------------N
304 residues (93.25%) of query sequence aligned
DONE: Mon Aug 18 04:16:52 2008 EST