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= 009562
(532 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 = 9e-06, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 35/63 (55%), Gaps = 7/63 (11%)
Query: 213 WITVHTKPCPKCHKPVEKNGGCNLVSC---ICGQAFCWLCGGATGRDHTWSRIAGHSCGR 269
WI +TK CPKCH +EK+GGCN + C C FCW+C G + A ++C R
Sbjct: 1 WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGS----AWYNCNR 56
Query: 270 YKE 272
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 = 33.1 bits (74), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 10/114 (8%)
Query: 302 FKLESKLKETVLEKVSISEERESRLR-------DFSWVTNGLYR---LFRSRRVLSYSYP 351
F + L E V E++ I R +R F+W+T YR L R S Y
Sbjct: 173 FGTQKLLAEXVTERLGIEVPRREDIRVNVLGINHFTWITKASYRHIDLLPIFREFSAHYG 232
Query: 352 FAFYMFGEELFKDEMTDEEREIKQHLFEDQQQQLEANVEKLSKFLEEPFDQYPD 405
+ 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 = 0.84, Method: Compositional matrix adjust.
Identities = 40/141 (28%), Positives = 57/141 (40%), Gaps = 27/141 (19%)
Query: 235 NLVSCICGQAFCWLCGGATG-RDHTWSRIAGHSCGRYKEDKAKKTERAKRELYRYMHYHN 293
NL S + A +L G +G RD +++IA S Y+ YM N
Sbjct: 353 NLYSRVVNMAHKFLGGEVSGARDEEYAKIAQESIKNYE---------------NYMEKVN 397
Query: 294 RYKAHTDSFKLESKLKETVLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSY-SYPF 352
YKA + K S L + V EK + +E + + V LY L VL++ YP
Sbjct: 398 FYKAIEEILKFTSYLNKYVDEKQPWALNKERKKEELQKV---LYALVDGLFVLTHLLYPI 454
Query: 353 -------AFYMFGEELFKDEM 366
A M GE+ F E+
Sbjct: 455 TPNKMKEALQMLGEKEFLKEL 475
>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 = 2.5, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 59 VMCDICMEEVAGDKATKMDCGHCFCNDCWT-EHFIVKINEGQS 100
V C IC+E + + +DCGH FC C T H +++G+S
Sbjct: 20 VTCPICLELLT--QPLSLDCGHSFCQACLTANHKKSMLDKGES 60
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 30.4 bits (67), Expect = 2.8, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 14/57 (24%)
Query: 54 PLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHKC 110
PL S C IC+ +A +A + CGH FC C K IR HKC
Sbjct: 2 PLGSKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHKC 44
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 86
L S +MC IC++ + TK +C H FC DC
Sbjct: 51 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 81
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 89
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 = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTE 89
L V+C IC++ + K +DCGH FC C T+
Sbjct: 17 LQEEVICPICLDIL--QKPVTIDCGHNFCLKCITQ 49
>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 = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 312 VLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDE-- 369
++ + +S ++ + + +F + L + F S RVL YS+ F +FGE+ + D
Sbjct: 2700 IVAQAQLSNQQSTIVSNFRKIL--LMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMAN 2757
Query: 370 --EREIK 374
E+E+K
Sbjct: 2758 IVEKEVK 2764
>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 = 4.2, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 50 DPMLPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHK 109
DP PL S C IC+ +A +A + CGH FC C K IR HK
Sbjct: 19 DP--PLESKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHK 62
Query: 110 C 110
C
Sbjct: 63 C 63
>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 = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 312 VLEKVSISEERESRLRDFSWVTNGLYRLFRSRRVLSYSYPFAFYMFGEELFKDEMTDE-- 369
++ + +S ++ + + +F + L + F S RVL YS+ F +FGE+ + D
Sbjct: 2578 IVAQAQLSNQQSTIVSNFRKIL--LMKAFHSDRVLQYSHSFVCSVFGEDFLNTQELDMAN 2635
Query: 370 --EREIK 374
E+E+K
Sbjct: 2636 IVEKEVK 2642
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 29.6 bits (65), Expect = 4.5, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 51 PMLPLSSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 86
P+ S TV C ICM+ + G +CGH FC+ C
Sbjct: 65 PIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 105
Score = 29.3 bits (64), Expect = 6.0, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 56 SSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 86
S TV C ICM+ + G +CGH FC+ C
Sbjct: 5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 40
>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: 375 QHLFEDQQQQLEANVEKLSKFLEEPFDQYPDDKVMEIRMQVINLSVITDTLCKKMYECIE 434
Q Q Q++ A V+K++KFL + F V++LS + + E
Sbjct: 65 QSTINQQSQEVGAMVDKIAKFLHDAF------------AAVVDLSKLAAIILNTFTNLEE 112
Query: 435 NDLLGCLQLGTHNIARYQS 453
G LQ T+N+ + S
Sbjct: 113 ESSSGFLQFNTNNVKKNSS 131
>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 = 29.3 bits (64), Expect = 5.3, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 56 SSTVMCDICMEEVA-----GDKATKMDCGHCFCNDC 86
S TV C ICM+ + G +CGH FC+ C
Sbjct: 8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 43
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 86
L S +MC IC++ + TK +C H FC DC
Sbjct: 50 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 80
>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 = 5.8, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 50 DPMLPLSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHFIVKINEGQSKRIRCMAHK 109
DP PL S C IC+ +A +A + CGH FC C K IR HK
Sbjct: 12 DP--PLESKYECPICL--MALREAVQTPCGHRFCKACII------------KSIRDAGHK 55
Query: 110 C 110
C
Sbjct: 56 C 56
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 29.3 bits (64), Expect = 6.4, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDCWTEHF 91
L+ ++C IC + D T +C H FC C HF
Sbjct: 12 LTPYILCSICKGYLI-DATTITECLHTFCKSCIVRHF 47
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 55 LSSTVMCDICMEEVAGDKATKMDCGHCFCNDC 86
L S +MC IC++ + TK +C H FC DC
Sbjct: 31 LHSELMCPICLDMLKNTMTTK-ECLHRFCADC 61
>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 = 28.5 bits (62), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 31/138 (22%), Positives = 56/138 (40%), Gaps = 15/138 (10%)
Query: 225 HKPVEKNGGCNLVSCICGQAFCWLCGGATG-RDHTWSRIAGHSCGRYKEDKAKKTERAKR 283
+ PV++ G I A W+ G G R I Y + +++ R +
Sbjct: 332 YGPVDQAGESPAYQAIADAAKGWIARGVDGLRLDAVKHI-------YHSETSEENPRFLK 384
Query: 284 ELYRYMHYHNRYKAHTDSFKLESKLKETVLEKVSISEERESRLRDFS------WVTNGLY 337
Y M+ + + K HTD F + ++ + +KV+ + L +FS W N
Sbjct: 385 MFYEDMNAYYKQKGHTDDFYMIGEVL-SEYDKVAPYYKGLPALFEFSFWYRLEWGINNST 443
Query: 338 RLFRSRRVLSYSYPFAFY 355
+ ++ +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
0.321 0.134 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,518,132
Number of Sequences: 62578
Number of extensions: 606610
Number of successful extensions: 1695
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 1679
Number of HSP's gapped (non-prelim): 48
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)