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= psy13254
(132 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
Length = 1022
Score = 139 bits (351), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 66/136 (48%), Positives = 99/136 (72%), Gaps = 8/136 (5%)
Query: 3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
+AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++ + + RVVRREIC+
Sbjct: 118 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 177
Query: 62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
I +G QT+S+++ D + +K+LL + KE D GVCF+DT++G+F +G+F D
Sbjct: 178 IITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSD 237
Query: 115 DKQFSRLSTLMSHYPP 130
D+ SR TL++HYPP
Sbjct: 238 DRHCSRFRTLVAHYPP 253
>pdb|1NNE|A Chain A, Crystal Structure Of The Muts-adpbef3-dna Complex
pdb|1NNE|B Chain B, Crystal Structure Of The Muts-adpbef3-dna Complex
Length = 765
Score = 42.7 bits (99), Expect = 6e-05, Method: Composition-based stats.
Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
+G P ++ +A+ L++ G+++A +Q E AE + + +VRRE+ ++
Sbjct: 71 AGIPLRAFEAYAERLLKMGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66 GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
G S++ +ANY L GD G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155
>pdb|1EWQ|A Chain A, Crystal Structure Taq Muts Complexed With A Heteroduplex
Dna At 2.2 A Resolution
pdb|1EWQ|B Chain B, Crystal Structure Taq Muts Complexed With A Heteroduplex
Dna At 2.2 A Resolution
Length = 765
Score = 42.7 bits (99), Expect = 6e-05, Method: Composition-based stats.
Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
+G P ++ +A+ L++ G+++A +Q E AE + + +VRRE+ ++
Sbjct: 71 AGIPLRAFEAYAERLLKXGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66 GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
G S++ +ANY L GD G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155
>pdb|1FW6|A Chain A, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex
pdb|1FW6|B Chain B, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex
Length = 768
Score = 42.4 bits (98), Expect = 7e-05, Method: Composition-based stats.
Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6 SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
+G P ++ +A+ L++ G+++A +Q E AE + + +VRRE+ ++
Sbjct: 71 AGIPLRAFEAYAERLLKXGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66 GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
G S++ +ANY L GD G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155
>pdb|3THW|B Chain B, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|B Chain B, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|B Chain B, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|B Chain B, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 918
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 38/130 (29%), Positives = 52/130 (40%), Gaps = 20/130 (15%)
Query: 20 LVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDV-DAN 78
LV KGYKV V+QTE+A I R + R + K T G ++ + DA
Sbjct: 81 LVAKGYKVGVVKQTETAALKAIGDNRSSL--FSRKLTALYTKSTLIGEDVNPLIKLDDAV 138
Query: 79 YVD-------NKFLLGVT--KEGDR--------LGVCFIDTTIGEFHVGEFEDDKQFSRL 121
VD +LL ++ KE R +G+ + GE F+D S L
Sbjct: 139 NVDEIMTDTSTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSASRSEL 198
Query: 122 STLMSHYPPC 131
T MS P
Sbjct: 199 ETRMSSLQPV 208
>pdb|4HCH|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCH|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Tartrate
pdb|4HCL|A Chain A, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
pdb|4HCL|B Chain B, Crystal Structure Of D-Glucarate Dehydratase From
Agrobacterium Tumefaciens Complexed With Magnesium And
L-Lyxarohydroxamate
Length = 402
Score = 29.3 bits (64), Expect = 0.62, Method: Composition-based stats.
Identities = 12/18 (66%), Positives = 16/18 (88%), Gaps = 1/18 (5%)
Query: 9 PEISYGKFAQTLVEKGYK 26
PE YG+FA+TLV++GYK
Sbjct: 170 PE-DYGRFAETLVKRGYK 186
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 94 RLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPP 130
++GV ++D+ + + EF D+ QFS L L+ P
Sbjct: 160 QVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGP 196
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 94 RLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPP 130
++GV ++D+ + + EF D+ QFS L L+ P
Sbjct: 160 QVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGP 196
>pdb|1RVK|A Chain A, Crystal Structure Of Enolase Agr_l_2751 From Agrobacterium
Tumefaciens
Length = 382
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%), Gaps = 1/18 (5%)
Query: 9 PEISYGKFAQTLVEKGYK 26
PE YG+FA+TLV++GYK
Sbjct: 150 PE-DYGRFAETLVKRGYK 166
>pdb|3BE4|A Chain A, Crystal Structure Of Cryptosporidium Parvum Adenylate
Kinase Cgd5_3360
Length = 217
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 54 VVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVC 98
++R I T G + SI++ N+V ++ +LG+ KE LGVC
Sbjct: 39 MLREAIKNGTKIGLEAKSIIE-SGNFVGDEIVLGLVKEKFDLGVC 82
>pdb|1V5E|A Chain A, Crystal Structure Of Pyruvate Oxidase Containing Fad, From
Aerococcus Viridans
pdb|2DJI|A Chain A, Crystal Structure Of Pyruvate Oxidase From Aerococcus
Viridans Containing Fad
Length = 590
Score = 25.8 bits (55), Expect = 7.8, Method: Composition-based stats.
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 8 FPEISYGKFAQTLVEKGYKVARVEQTE 34
F ++ Y K A+ KG+ V+R+E +
Sbjct: 489 FTDVDYAKIAEAQGAKGFTVSRIEDMD 515
>pdb|1V5F|A Chain A, Crystal Structure Of Pyruvate Oxidase Complexed With Fad
And Tpp, From Aerococcus Viridans
pdb|1V5G|A Chain A, Crystal Structure Of The Reaction Intermediate Between
Pyruvate Oxidase Containing Fad And Tpp, And Substrate
Pyruvate
Length = 589
Score = 25.8 bits (55), Expect = 7.8, Method: Composition-based stats.
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 8 FPEISYGKFAQTLVEKGYKVARVEQTE 34
F ++ Y K A+ KG+ V+R+E +
Sbjct: 488 FTDVDYAKIAEAQGAKGFTVSRIEDMD 514
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 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,716,031
Number of Sequences: 62578
Number of extensions: 131361
Number of successful extensions: 295
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 274
Number of HSP's gapped (non-prelim): 16
length of query: 132
length of database: 14,973,337
effective HSP length: 88
effective length of query: 44
effective length of database: 9,466,473
effective search space: 416524812
effective search space used: 416524812
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: 46 (22.3 bits)