BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 007785
(590 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
Ring (Triad) Motif
Length = 60
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 271 WITVHTKPCPKCHKPVEKNGGCNLVSC---ICGQAFCWLCGGATGRDHTWSRIAGHSCGR 327
WI +TK CPKCH +EK+GGCN + C C FCW+C G + A ++C R
Sbjct: 1 WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGS----AWYNCNR 56
Query: 328 YKE 330
Y E
Sbjct: 57 YNE 59
>pdb|3FEF|A Chain A, Crystal Structure Of Putative Glucosidase Lpld From
Bacillus Subtilis
pdb|3FEF|B Chain B, Crystal Structure Of Putative Glucosidase Lpld From
Bacillus Subtilis
pdb|3FEF|C Chain C, Crystal Structure Of Putative Glucosidase Lpld From
Bacillus Subtilis
pdb|3FEF|D Chain D, Crystal Structure Of Putative Glucosidase Lpld From
Bacillus Subtilis
Length = 450
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 10/114 (8%)
Query: 360 FKLESKLKETVLEKVSISEERESRLR-------DFSWVTNGLYR---LFRSRRVLSYSYP 409
F + L E V E++ I R +R F+W+T YR L R S Y
Sbjct: 173 FGTQKLLAEXVTERLGIEVPRREDIRVNVLGINHFTWITKASYRHIDLLPIFREFSAHYG 232
Query: 410 FAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPD 463
+ Y E ++D + + LFE A L++FL P+ + P+
Sbjct: 233 ESGYELEGECWRDSVFCSAHRVAFDLFETYGAIPAAGDRHLAEFLPGPYLKQPE 286
>pdb|2CSX|A Chain A, Crystal Structure Of Aquifex Aeolicus Methionyl-Trna
Synthetase Complexed With Trna(Met)
pdb|2CSX|B Chain B, Crystal Structure Of Aquifex Aeolicus Methionyl-Trna
Synthetase Complexed With Trna(Met)
pdb|2CT8|A Chain A, Crystal Structure Of Aquifex Aeolicus Methionyl-Trna
Synthetase Complexed With Trna(Met) And
Methionyl-Adenylate Anologue
pdb|2CT8|B Chain B, Crystal Structure Of Aquifex Aeolicus Methionyl-Trna
Synthetase Complexed With Trna(Met) And
Methionyl-Adenylate Anologue
Length = 497
Score = 32.0 bits (71), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 40/141 (28%), Positives = 57/141 (40%), Gaps = 27/141 (19%)
Query: 293 NLVSCICGQAFCWLCGGATG-RDHTWSRIAGHSCGRYKEDKAKKTERAKRELYRYMHYHN 351
NL S + A +L G +G RD +++IA S Y+ YM N
Sbjct: 353 NLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYE---------------NYMEKVN 397
Query: 352 RYKAHTDSFKLESKLKETVLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSY-SYPF 410
YKA + K S L + V EK + +E + + V LY L VL++ YP
Sbjct: 398 FYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKV---LYALVDGLFVLTHLLYPI 454
Query: 411 -------AFYMFGEELFKDEM 424
A M GE+ F E+
Sbjct: 455 TPNKMKEALQMLGEKEFLKEL 475
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 14/57 (24%)
Query: 112 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKC 168
PL S C IC+ +A +A + CGH FC C K IR HKC
Sbjct: 2 PLGSKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHKC 44
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 147
L V+C IC++ + K +DCGH FC C T+
Sbjct: 17 LQEEVICPICLDIL--QKPVTIDCGHNFCLKCITQ 49
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 147
L V+C IC++ + K +DCGH FC C T+
Sbjct: 17 LQEEVICPICLDIL--QKPVTIDCGHNFCLKCITQ 49
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144
L S +MC IC++ + TK +C H FC DC
Sbjct: 51 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 81
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 117 VMCDICMEEVAGDKATKMDCGHCFCNDCWT 146
V C IC+E + + +DCGH FC C T
Sbjct: 20 VTCPICLELLT--QPLSLDCGHSFCQACLT 47
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 30.0 bits (66), Expect = 3.5, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 109 PMLPLSSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 144
P+ S TV C ICM+ + G +CGH FC+ C
Sbjct: 65 PIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 105
Score = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 114 SSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 144
S TV C ICM+ + G +CGH FC+ C
Sbjct: 5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 40
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 114 SSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 144
S TV C ICM+ + G +CGH FC+ C
Sbjct: 8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 43
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 370 VLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDE-- 427
++ + +S ++ + + +F + L + F S RVL YS+ F +FGE+ + D
Sbjct: 2700 IVAQAQLSNQQSTIVSNFRKIL--LMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMAN 2757
Query: 428 --EREIK 432
E+E+K
Sbjct: 2758 IVEKEVK 2764
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 370 VLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDE-- 427
++ + +S ++ + + +F + L + F S RVL YS+ F +FGE+ + D
Sbjct: 2578 IVAQAQLSNQQSTIVSNFRKIL--LMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMAN 2635
Query: 428 --EREIK 432
E+E+K
Sbjct: 2636 IVEKEVK 2642
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 29.6 bits (65), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 14/57 (24%)
Query: 112 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKC 168
PL S C IC+ +A +A + CGH FC C K IR HKC
Sbjct: 21 PLESKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHKC 63
>pdb|1PP0|A Chain A, Volvatoxin A2 In Monoclinic Crystal
pdb|1PP0|B Chain B, Volvatoxin A2 In Monoclinic Crystal
pdb|1PP0|C Chain C, Volvatoxin A2 In Monoclinic Crystal
pdb|1PP0|D Chain D, Volvatoxin A2 In Monoclinic Crystal
pdb|1PP6|A Chain A, Vva2 (Strip Crystal Form)
pdb|1PP6|B Chain B, Vva2 (Strip Crystal Form)
pdb|1PP6|C Chain C, Vva2 (Strip Crystal Form)
pdb|1PP6|D Chain D, Vva2 (Strip Crystal Form)
pdb|1PP6|E Chain E, Vva2 (Strip Crystal Form)
pdb|1VGF|A Chain A, Volvatoxin A2 (Diamond Crystal Form)
pdb|1VGF|B Chain B, Volvatoxin A2 (Diamond Crystal Form)
Length = 199
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 433 QHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 492
Q Q Q++ A V+K++KFL + F V++LS + + E
Sbjct: 65 QSTINQQSQEVGAMVDKIAKFLHDAF------------AAVVDLSKLAAIILNTFTNLEE 112
Query: 493 NDLLGCLQLGTHNIARYQS 511
G LQ T+N+ + S
Sbjct: 113 ESSSGFLQFNTNNVKKNSS 131
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 29.6 bits (65), Expect = 5.1, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHF 149
L+ ++C IC + D T +C H FC C HF
Sbjct: 12 LTPYILCSICKGYLI-DATTITECLHTFCKSCIVRHF 47
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144
L S +MC IC++ + TK +C H FC DC
Sbjct: 50 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 80
>pdb|4ACK|A Chain A, 3d Structure Of Dotu From Francisella Novicida
pdb|4ACK|B Chain B, 3d Structure Of Dotu From Francisella Novicida
Length = 185
Score = 29.6 bits (65), Expect = 5.5, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 418 ELFKDEMTDEER------EIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIR 470
E+ +D D E+ I++ +F Q++ LE E + K++ P Y D+K+M +R
Sbjct: 19 EIIEDNDNDNEKISYHRNNIRKSIFFLQEELLEKYSETVCKYIVFPLLAYVDEKLMLLR 77
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 113 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 144
L S +MC IC++ + TK +C H FC DC
Sbjct: 31 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 61
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 108 DPMLPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHK 167
DP PL S C IC+ +A +A + CGH FC C K IR HK
Sbjct: 12 DP--PLESKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHK 55
Query: 168 C 168
C
Sbjct: 56 C 56
>pdb|2NTY|A Chain A, Rop4-Gdp-Prone8
pdb|2NTY|B Chain B, Rop4-Gdp-Prone8
pdb|2WBL|A Chain A, Three-Dimensional Structure Of A Binary Rop-Prone Complex
pdb|2WBL|B Chain B, Three-Dimensional Structure Of A Binary Rop-Prone Complex
Length = 365
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 8/44 (18%)
Query: 3 DSFSGDEDYYYSDRDSLDGLE--NDEADLQW------VPPKGSS 38
D+F G +++Y RDS +G + ND + +W VPP G S
Sbjct: 129 DNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLS 172
>pdb|2NTX|A Chain A, Prone8
pdb|2NTX|B Chain B, Prone8
Length = 365
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 8/44 (18%)
Query: 3 DSFSGDEDYYYSDRDSLDGLE--NDEADLQW------VPPKGSS 38
D+F G +++Y RDS +G + ND + +W VPP G S
Sbjct: 129 DNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLS 172
>pdb|1NXC|A Chain A, Structure Of Mouse Golgi Alpha-1,2-Mannosidase Ia Reveals
The Molecular Basis For Substrate Specificity Among
Class I Enzymes (Family 47 Glycosidases)
Length = 478
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 31 WVPPKGSSTKVITRESLLAAQKEDLRRVMELLSLREHHARTLLIHYRWDVEKLLAVLVEN 90
++PP G V RE A +E ++ E+++ HA Y W + +L + E
Sbjct: 1 FLPPVG----VENREPADATIREKRAKIKEMMT----HAWNNYKRYAWGLNELKPISKEG 52
Query: 91 GKESLF-NEAGVTVIDDADPML 111
SLF N G T++D D +
Sbjct: 53 HSSSLFGNIKGATIVDALDTLF 74
>pdb|3K8L|A Chain A, Crystal Structure Of Susg-D498n Mutant With Maltoheptaose
pdb|3K8L|B Chain B, Crystal Structure Of Susg-D498n Mutant With Maltoheptaose
Length = 669
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 31/138 (22%), Positives = 56/138 (40%), Gaps = 15/138 (10%)
Query: 283 HKPVEKNGGCNLVSCICGQAFCWLCGGATG-RDHTWSRIAGHSCGRYKEDKAKKTERAKR 341
+ PV++ G I A W+ G G R I Y + +++ R +
Sbjct: 332 YGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHI-------YHSETSEENPRFLK 384
Query: 342 ELYRYMHYHNRYKAHTDSFKLESKLKETVLEKVSISEERESRLRDFS------WVTNGLY 395
Y M+ + + K HTD F + ++ + +KV+ + L +FS W N
Sbjct: 385 MFYEDMNAYYKQKGHTDDFYMIGEVL-SEYDKVAPYYKGLPALFEFSFWYRLEWGINNST 443
Query: 396 RLFRSRRVLSYSYPFAFY 413
+ ++ +LSY +A Y
Sbjct: 444 GCYFAKDILSYQQKYANY 461
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.134 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,385,658
Number of Sequences: 62578
Number of extensions: 683572
Number of successful extensions: 1929
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 1912
Number of HSP's gapped (non-prelim): 44
length of query: 590
length of database: 14,973,337
effective HSP length: 104
effective length of query: 486
effective length of database: 8,465,225
effective search space: 4114099350
effective search space used: 4114099350
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)