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= psy13391
(146 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 106 bits (264), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 56/134 (41%), Positives = 81/134 (60%), Gaps = 1/134 (0%)
Query: 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCY 60
+KQPL D + I ER V V + E R L E LR PD+ LA + R+ A L+DCY
Sbjct: 346 IKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAANLQDCY 405
Query: 61 RVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHS 120
R+Y+G++QLP +I LE + L ++ L L +D +KFQEMIETT+D+++ +
Sbjct: 406 RLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVEN 465
Query: 121 EREFFIRPSFDEDL 134
EF ++PSFD +L
Sbjct: 466 -HEFLVKPSFDPNL 478
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 106 bits (264), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 56/134 (41%), Positives = 81/134 (60%), Gaps = 1/134 (0%)
Query: 1 MKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCY 60
+KQPL D + I ER V V + E R L E LR PD+ LA + R+ A L+DCY
Sbjct: 346 IKQPLMDKNRIEERLNLVEAFVEDAELRQTLQEDLLRRFPDLNRLAKKFQRQAANLQDCY 405
Query: 61 RVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHS 120
R+Y+G++QLP +I LE + L ++ L L +D +KFQEMIETT+D+++ +
Sbjct: 406 RLYQGINQLPNVIQALEKHEGKHQKLLLAVFVTPLTDLRSDFSKFQEMIETTLDMDQVEN 465
Query: 121 EREFFIRPSFDEDL 134
EF ++PSFD +L
Sbjct: 466 -HEFLVKPSFDPNL 478
>pdb|3P8C|A Chain A, Structure And Control Of The Actin Regulatory Wave Complex
Length = 1253
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 34/114 (29%), Positives = 51/114 (44%), Gaps = 23/114 (20%)
Query: 35 ALRGLPDMQS-LAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLVQNVEASNLNTILS 93
ALRG D +S +++ R+ G +QL + ++LESL+ + S T+ S
Sbjct: 532 ALRGEKDPKSGFDIKVPRRAVG--------PSSTQLYMVRTMLESLIADKSGSK-KTLRS 582
Query: 94 SLQSLSNDLAKFQEMIETTIDIERFHSEREFFIR-PSFDEDLQGKAIKSNLKSR 146
SL+ T +DIE+FH E F+ +F E LQ S L R
Sbjct: 583 SLEG------------PTILDIEKFHRESFFYTHLINFSETLQQCCDLSQLWFR 624
>pdb|2BL0|B Chain B, Physarum Polycephalum Myosin Ii Regulatory Domain
Length = 145
Score = 29.6 bits (65), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 56 LKDCYRVYE----GVSQLPKLISILESLVQNVEASNLNTILSSLQSLSNDLAKFQ 106
+++C+++++ G + +L S L SL +N + LNTI L + DLA F+
Sbjct: 7 IQECFQIFDKDNDGKVSIEELGSALRSLGKNPTNAELNTIKGQLNAKEFDLATFK 61
>pdb|3DP7|A Chain A, Crystal Structure Of Sam-Dependent Methyltransferase From
Bacteroides Vulgatus Atcc 8482
pdb|3DP7|B Chain B, Crystal Structure Of Sam-Dependent Methyltransferase From
Bacteroides Vulgatus Atcc 8482
Length = 363
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 8/63 (12%)
Query: 17 AVNILVNNTEARMNL---HEYALRGLPDMQSLAMRIGRKKAGLK---DCYRVYEGVSQLP 70
A L+N+ AR+N+ H+ +GL ++ A+ GR + GLK + +YEG+SQLP
Sbjct: 92 AGWFLLNDKMARVNMEFNHDVNYQGLFHLEE-ALLNGRPE-GLKVFGEWPTIYEGLSQLP 149
Query: 71 KLI 73
+ +
Sbjct: 150 EQV 152
>pdb|2E87|A Chain A, Crystal Structure Of Hypothetical Gtp-Binding Protein
Ph1320 From Pyrococcus Horikoshii Ot3, In Complex With
Gdp
Length = 357
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 80 VQNVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFH 119
V NV NL +L LS +QE+++ +D + FH
Sbjct: 53 VSNVVRDNLRKVLERTPGLSTLPKFYQELVDVLVDRDTFH 92
>pdb|4H63|H Chain H, Structure Of The Schizosaccharomyces Pombe Mediator Head
Module
Length = 200
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 87 NLNTILSSLQSLSNDLAKFQEMIETT 112
N N +LS + SLSN+LA ++TT
Sbjct: 49 NFNILLSQIHSLSNNLAAHSHTLQTT 74
>pdb|3ZBH|A Chain A, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|B Chain B, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|C Chain C, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|D Chain D, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|E Chain E, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|F Chain F, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|G Chain G, Geobacillus Thermodenitrificans Esxa Crystal Form I
pdb|3ZBH|H Chain H, Geobacillus Thermodenitrificans Esxa Crystal Form I
Length = 99
Score = 26.6 bits (57), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 82 NVEASNLNTILSSLQSLSNDLAKFQEMIETTIDIERFHSEREFFIRPSFD 131
NVE+SN+ +++ L +S+ L E + I+++ +RPSF+
Sbjct: 22 NVESSNVTELIARLDQMSHTLQGIWEGASSEAFIQQYQE-----LRPSFE 66
>pdb|5TNC|A Chain A, Refined Crystal Structure Of Troponin C From Turkey
Skeletal Muscle At 2.0 Angstroms Resolution
Length = 162
Score = 26.2 bits (56), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/96 (20%), Positives = 47/96 (48%), Gaps = 13/96 (13%)
Query: 2 KQPLKD-LDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCY 60
+ P K+ LDAI+E + + ++ E+ + + M+ A G+ + L+DC+
Sbjct: 51 QNPTKEELDAIIEE------VDEDGSGTIDFEEFLVMMVRQMKEDAK--GKSEEELEDCF 102
Query: 61 RVY----EGVSQLPKLISILESLVQNVEASNLNTIL 92
R++ +G + +L IL + ++V ++ ++
Sbjct: 103 RIFDKNADGFIDIEELGEILRATGEHVTEEDIEDLM 138
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
0.318 0.133 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,475,371
Number of Sequences: 62578
Number of extensions: 111865
Number of successful extensions: 367
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 21
length of query: 146
length of database: 14,973,337
effective HSP length: 90
effective length of query: 56
effective length of database: 9,341,317
effective search space: 523113752
effective search space used: 523113752
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)