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= psy8409
(937 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 95.9 bits (237), Expect = 8e-20, Method: Composition-based stats.
Identities = 39/64 (60%), Positives = 54/64 (84%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRRQMFF 78
CKTCIV+YL+ KYCPICDV V+KT+PL +IR D LQ++VYKL+PGL++ EM+RR+ F+
Sbjct: 39 CKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFY 98
Query: 79 SSTP 82
++ P
Sbjct: 99 AAHP 102
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 95.5 bits (236), Expect = 1e-19, Method: Composition-based stats.
Identities = 39/64 (60%), Positives = 54/64 (84%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRRQMFF 78
CKTCIV+YL+ KYCPICDV V+KT+PL +IR D LQ++VYKL+PGL++ EM+RR+ F+
Sbjct: 39 CKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFY 98
Query: 79 SSTP 82
++ P
Sbjct: 99 AAHP 102
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 95.1 bits (235), Expect = 2e-19, Method: Composition-based stats.
Identities = 38/62 (61%), Positives = 53/62 (85%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRRQMFF 78
CKTCIV+YL+ KYCPICDV V+KT+PL +IR D LQ++VYKL+PGL++ EM+RR+ F+
Sbjct: 35 CKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFY 94
Query: 79 SS 80
++
Sbjct: 95 AA 96
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 21/28 (75%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPL 46
CK+CIV++ CP C+++V++T+PL
Sbjct: 39 CKSCIVRHFYYSNRCPKCNIVVHQTQPL 66
>pdb|2FQM|A Chain A, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
pdb|2FQM|B Chain B, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
pdb|2FQM|C Chain C, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
pdb|2FQM|D Chain D, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
pdb|2FQM|E Chain E, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
pdb|2FQM|F Chain F, Crystal Structure Of The Oligomerization Domain Of The
Phosphoprotein Of Vesicular Stomatitis Virus
Length = 75
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 282 GAHSNEWKEVELKINDNGVMSATVLPPVTSQTQNSSNLLNLTTQAQSKQQYGLIPVTSET 341
G+H +WK+ EL+ +++G LP S Q S +L + QS + + L T E
Sbjct: 1 GSHM-DWKQPELESDEHGKTLRLTLPEGLSGEQKSQWMLTIKAVVQSAKHWNLAECTFEA 59
Query: 342 S 342
S
Sbjct: 60 S 60
>pdb|3NAZ|A Chain A, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|B Chain B, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|C Chain C, Basal State Form Of Yeast Glycogen Synthase
pdb|3NAZ|D Chain D, Basal State Form Of Yeast Glycogen Synthase
pdb|3NCH|A Chain A, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|B Chain B, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|C Chain C, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3NCH|D Chain D, Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
pdb|3O3C|A Chain A, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|B Chain B, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|C Chain C, Glycogen Synthase Basal State Udp Complex
pdb|3O3C|D Chain D, Glycogen Synthase Basal State Udp Complex
pdb|3RSZ|A Chain A, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|B Chain B, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|C Chain C, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
pdb|3RSZ|D Chain D, Maltodextran Bound Basal State Conformation Of Yeast
Glycogen Synthase Isoform 2
Length = 725
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 52 DTRLQNVVYKLIPGLYEKEMQRRQMFFSSTPIQN-SLGLTGEDKGIITESSDIILPDENI 110
D L N +Y I G YE + + MF + N L ++G K ++ + I++P +N
Sbjct: 326 DFDLDNTLYFFIAGRYEYKNKGADMFIEALARLNYRLKVSGSKKTVV---AFIVMPAKNN 382
Query: 111 SITLEYL 117
S T+E L
Sbjct: 383 SFTVEAL 389
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 30.8 bits (68), Expect = 4.0, Method: Composition-based stats.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 19 CKTCIVKYLKRHKYCPIC 36
C+ CI K+ RH+ CPIC
Sbjct: 37 CQKCIDKWSDRHRNCPIC 54
>pdb|3NB0|A Chain A, Glucose-6-Phosphate Activated Form Of Yeast Glycogen
Synthase
pdb|3NB0|B Chain B, Glucose-6-Phosphate Activated Form Of Yeast Glycogen
Synthase
pdb|3NB0|C Chain C, Glucose-6-Phosphate Activated Form Of Yeast Glycogen
Synthase
pdb|3NB0|D Chain D, Glucose-6-Phosphate Activated Form Of Yeast Glycogen
Synthase
pdb|3RT1|A Chain A, Maltodextarn Bound Activated State Form Of Yeast Glycogen
Synthase Isoform 2
pdb|3RT1|B Chain B, Maltodextarn Bound Activated State Form Of Yeast Glycogen
Synthase Isoform 2
pdb|3RT1|C Chain C, Maltodextarn Bound Activated State Form Of Yeast Glycogen
Synthase Isoform 2
pdb|3RT1|D Chain D, Maltodextarn Bound Activated State Form Of Yeast Glycogen
Synthase Isoform 2
Length = 725
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 52 DTRLQNVVYKLIPGLYEKEMQRRQMFFSSTPIQN-SLGLTGEDKGIITESSDIILPDENI 110
D L N +Y I G YE + + MF + N L ++G K ++ + I++P +N
Sbjct: 326 DFDLDNTLYFFIAGRYEYKNKGADMFIEALARLNYRLKVSGSKKTVV---AFIVMPAKNN 382
Query: 111 SITLEYL 117
S T+E L
Sbjct: 383 SFTVEAL 389
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRR 74
C CI +++KR CPIC K ++S L N + K++ L + +RR
Sbjct: 76 CSYCINEWMKRKIECPIC------RKDIKSKTYSLVLDNCINKMVNNLSSEVKERR 125
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 30.4 bits (67), Expect = 4.7, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRR 74
C CI +++KR CPIC K ++S L N + K++ L + +RR
Sbjct: 87 CSYCINEWMKRKIECPIC------RKDIKSKTYSLVLDNCINKMVNNLSSEVKERR 136
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 30.4 bits (67), Expect = 4.9, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 19 CKTCIVKYLKRHKYCPICDVLVYKTKPLQSIRPDTRLQNVVYKLIPGLYEKEMQRR 74
C CI +++KR CPIC K ++S L N + K++ L + +RR
Sbjct: 76 CSYCINEWMKRKIECPIC------RKDIKSKTYSLVLDNXINKMVNNLSSEVKERR 125
>pdb|3V89|A Chain A, The Crystal Structure Of Transferrin Binding Protein A
(Tbpa) From Neisseria Meningitidis Serogroup B In
Complex With The C-Lobe Of Human Transferrin
Length = 904
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 535 TKVDPRTLSPIVPVSSSTTKVDSPTYIDNSTSPSHLSVDKHNKYARPSQIKEFNPFLHPS 594
T D T + +S V +DN +H S D +KY RPS K F+ +
Sbjct: 404 TNADKDTWADYARLSYDRQGVG----LDNHFQQTHCSADGSDKYCRPSADKPFSYYKSDR 459
Query: 595 IFYP 598
+ Y
Sbjct: 460 VIYG 463
>pdb|3V8X|A Chain A, The Crystal Structure Of Transferrin Binding Protein A
(Tbpa) From Neisserial Meningitidis Serogroup B In
Complex With Full Length Human Transferrin
Length = 904
Score = 30.0 bits (66), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 535 TKVDPRTLSPIVPVSSSTTKVDSPTYIDNSTSPSHLSVDKHNKYARPSQIKEFNPFLHPS 594
T D T + +S V +DN +H S D +KY RPS K F+ +
Sbjct: 404 TNADKDTWADYARLSYDRQGVG----LDNHFQQTHCSADGSDKYCRPSADKPFSYYKSDR 459
Query: 595 IFYP 598
+ Y
Sbjct: 460 VIYG 463
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
0.311 0.126 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,868,330
Number of Sequences: 62578
Number of extensions: 776504
Number of successful extensions: 1117
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1109
Number of HSP's gapped (non-prelim): 13
length of query: 937
length of database: 14,973,337
effective HSP length: 108
effective length of query: 829
effective length of database: 8,214,913
effective search space: 6810162877
effective search space used: 6810162877
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (26.2 bits)