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= 041658
(139 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
Minimized Mean Structure
pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
46 Structures
Length = 70
Score = 89.4 bits (220), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 44/61 (72%), Positives = 49/61 (80%), Gaps = 1/61 (1%)
Query: 27 RSFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGKKAKLNF 86
+ +RGVR+RPWGKF AEIRD NG RVWLGTF T EDAALAYDRAAFR+ G +A LNF
Sbjct: 4 KHYRGVRQRPWGKFAAEIRD-PAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 62
Query: 87 P 87
P
Sbjct: 63 P 63
>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
Structure
Length = 63
Score = 89.4 bits (220), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 44/61 (72%), Positives = 49/61 (80%), Gaps = 1/61 (1%)
Query: 27 RSFRGVRRRPWGKFGAEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHGKKAKLNF 86
+ +RGVR+RPWGKF AEIRD NG RVWLGTF T EDAALAYDRAAFR+ G +A LNF
Sbjct: 1 KHYRGVRQRPWGKFAAEIRD-PAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNF 59
Query: 87 P 87
P
Sbjct: 60 P 60
>pdb|2QA2|A Chain A, Crystal Structure Of Cabe, An Aromatic Hydroxylase From
Angucycline Biosynthesis, Determined To 2.7 A Resolution
Length = 499
Score = 28.1 bits (61), Expect = 1.8, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 47 GKD-NNGERVWLGTFYTPEDAALAYDRAAFRLHGKKAKLNFP 87
G+D ++GE VW+ F P AY R L G A ++ P
Sbjct: 251 GQDISHGEPVWVSAFGDPARQVSAYRRGRVLLAGDSAHVHLP 292
>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 = 27.3 bits (59), Expect = 2.8, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 42 AEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHG 79
+EI + D + +VWLG PE A ++A +L+G
Sbjct: 3091 SEISESSDYSSIQVWLGGLLNPEAYITATRQSASQLNG 3128
>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 = 27.3 bits (59), Expect = 2.9, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 42 AEIRDGKDNNGERVWLGTFYTPEDAALAYDRAAFRLHG 79
+EI + D + +VWLG PE A ++A +L+G
Sbjct: 3213 SEISESSDYSSIQVWLGGLLNPEAYITATRQSASQLNG 3250
>pdb|3PPC|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
pdb|3PPC|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Tyrosine Variant
With Zinc
Length = 789
Score = 26.9 bits (58), Expect = 3.7, Method: Composition-based stats.
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 62 TPEDAALAYDRAAF--RLHGKKAKLNFPRFVTDT 93
T + ALA +AAF RL +KAK N P F T T
Sbjct: 434 TTINEALATRKAAFPERLTEQKAKYNLPLFPTTT 467
>pdb|3PPH|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
pdb|3PPH|B Chain B, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Threonine Variant
Length = 789
Score = 26.9 bits (58), Expect = 3.8, Method: Composition-based stats.
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 62 TPEDAALAYDRAAF--RLHGKKAKLNFPRFVTDT 93
T + ALA +AAF RL +KAK N P F T T
Sbjct: 434 TTINEALATRKAAFPERLTEQKAKYNLPLFPTTT 467
>pdb|3PPF|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
Without Zinc
pdb|3PPG|A Chain A, Crystal Structure Of The Candida Albicans Methionine
Synthase By Surface Entropy Reduction, Alanine Variant
With Zinc
Length = 789
Score = 26.9 bits (58), Expect = 3.8, Method: Composition-based stats.
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 62 TPEDAALAYDRAAF--RLHGKKAKLNFPRFVTDT 93
T + ALA +AAF RL +KAK N P F T T
Sbjct: 434 TTINEALATRKAAFPERLTEQKAKYNLPLFPTTT 467
>pdb|3K6S|A Chain A, Structure Of Integrin Alphaxbeta2 Ectodomain
pdb|3K6S|C Chain C, Structure Of Integrin Alphaxbeta2 Ectodomain
pdb|3K6S|E Chain E, Structure Of Integrin Alphaxbeta2 Ectodomain
pdb|3K6S|G Chain G, Structure Of Integrin Alphaxbeta2 Ectodomain
pdb|3K71|A Chain A, Structure Of Integrin Alphax Beta2 Ectodomain
pdb|3K71|C Chain C, Structure Of Integrin Alphax Beta2 Ectodomain
pdb|3K71|E Chain E, Structure Of Integrin Alphax Beta2 Ectodomain
pdb|3K71|G Chain G, Structure Of Integrin Alphax Beta2 Ectodomain
pdb|3K72|A Chain A, Structure Of Integrin Alphax Beta2
pdb|3K72|C Chain C, Structure Of Integrin Alphax Beta2
Length = 1095
Score = 26.9 bits (58), Expect = 3.8, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 9/39 (23%)
Query: 26 PRSFR---------GVRRRPWGKFGAEIRDGKDNNGERV 55
PR +R G + PWG+FGA + D NG+++
Sbjct: 479 PRGWRRWWCDAVLYGEQGHPWGRFGAALTVLGDVNGDKL 517
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 0.136 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,249,216
Number of Sequences: 62578
Number of extensions: 116949
Number of successful extensions: 275
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 10
length of query: 139
length of database: 14,973,337
effective HSP length: 89
effective length of query: 50
effective length of database: 9,403,895
effective search space: 470194750
effective search space used: 470194750
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)