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= 029921
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 75 GFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSN 134
GFL R E+ SL K + +Q +D QI+ D+ RT+P + + S
Sbjct: 59 GFLQRKR---KEYRDSL-KHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSV----- 109
Query: 135 QEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSD 172
Q +L+ IL ++A +P YVQG+N+++ P + F ++
Sbjct: 110 QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTE 147
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 75 GFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSN 134
GFL R E+ SL K + +Q +D QI+ D+ RT+P + + S
Sbjct: 79 GFLQRKR---KEYRDSL-KHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSV----- 129
Query: 135 QEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSD 172
Q +L+ IL ++A +P YVQG+N+++ P + F ++
Sbjct: 130 QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTE 167
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 109 QIDRDVKRTHPDMHFFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYV 168
QI D+ RT+P + F QE + IL ++A +P YVQG+N+++ P + V
Sbjct: 108 QIHIDIPRTNPLIPLFQQPLV-----QEIFERILFIWAIRHPASGYVQGINDLVTPFFVV 162
Query: 169 FKSDPDEE 176
F S+ EE
Sbjct: 163 FLSEYVEE 170
>pdb|2QFZ|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 22a
pdb|2QFZ|B Chain B, Crystal Structure Of Human Tbc1 Domain Family Member 22a
Length = 345
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 42/179 (23%), Positives = 66/179 (36%), Gaps = 55/179 (30%)
Query: 3 GIPDGAGIRSTVWKLLLVYLPPDRGLWPSELAKKRSQYKHFKDDLLVNPSEITRRLDKST 62
GIP +R WKLL YLP + P+ L +K+ +Y F +
Sbjct: 50 GIP--KPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHY--------------- 92
Query: 63 IYESEEWKCESSGFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMH 122
+ SR++ H QD+ QI D+ R P+
Sbjct: 93 -------------YDSRNDEVH-----------------QDT--YRQIHIDIPRMSPEAL 120
Query: 123 FFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSDPDEEFSVST 181
+ E + IL ++A +P YVQG+N+++ P + VF + E V T
Sbjct: 121 ILQPKVT------EIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDT 173
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 34.3 bits (77), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 49/118 (41%), Gaps = 19/118 (16%)
Query: 50 NPSEITRRL-DKSTIYESEEWKCESSGFLSRSEITHDEHPLSLGKSSIWNQFFQDSEI-M 107
N IT L D E W+ S+G SE+ +++ S D E +
Sbjct: 64 NELNITHELFDICLARAKERWRSLSTG---GSEVENEDAGFSAA----------DREASL 110
Query: 108 EQIDRDVKRTHPDMHFFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPL 165
E I D+ RT P++ F + + L +IL + P + YVQGM+ I A L
Sbjct: 111 ELIKLDISRTFPNLCIFQQGGPY----HDMLHSILGAYTCYRPDVGYVQGMSFIAAVL 164
>pdb|3PGY|A Chain A, Serine Hydroxymethyltransferase From Staphylococcus
Aureus, S95p Mutant.
pdb|3PGY|B Chain B, Serine Hydroxymethyltransferase From Staphylococcus
Aureus, S95p Mutant.
pdb|3PGY|C Chain C, Serine Hydroxymethyltransferase From Staphylococcus
Aureus, S95p Mutant.
pdb|3PGY|D Chain D, Serine Hydroxymethyltransferase From Staphylococcus
Aureus, S95p Mutant
Length = 415
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 102 QDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSNQEALKNILI-VFAKLNPGIRYVQG 157
QD I E I+R+ +R + ++ + ++ + + EA ++L +A+ PG RY G
Sbjct: 10 QDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRYYGG 66
>pdb|3QYE|A Chain A, Crystal Structure Of Human Tbc1d1 Rabgap Domain
pdb|3QYE|B Chain B, Crystal Structure Of Human Tbc1d1 Rabgap Domain
Length = 331
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/119 (21%), Positives = 48/119 (40%), Gaps = 8/119 (6%)
Query: 64 YESEEWKCESSGFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHF 123
+ E WK + F + + + P + + Q + I D+ RT P +
Sbjct: 64 HRGEIWKFLAEQFHLKHQFPSKQQPKDVPYKELLKQL---TSQQHAILIDLGRTFPTHPY 120
Query: 124 FSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSDPDEEFSVSTF 182
FS + Q +L NIL ++ L+ + Y QG++ + L + +E F + F
Sbjct: 121 FSAQLG---AGQLSLYNILKAYSLLDQEVGYCQGLSFVAGIL--LLHMSEEEAFKMLKF 174
>pdb|2B67|A Chain A, Crystal Structure Of The Nitroreductase Family Protein
From Streptococcus Pneumoniae Tigr4
pdb|2B67|B Chain B, Crystal Structure Of The Nitroreductase Family Protein
From Streptococcus Pneumoniae Tigr4
pdb|2B67|C Chain C, Crystal Structure Of The Nitroreductase Family Protein
From Streptococcus Pneumoniae Tigr4
pdb|2B67|D Chain D, Crystal Structure Of The Nitroreductase Family Protein
From Streptococcus Pneumoniae Tigr4
Length = 204
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 32 ELAKKRSQYKHFKDDLLVNPSEITRRLDKSTI----YESEEWK 70
EL KKR KHF D LV+P ++ ++ +T+ + S+ WK
Sbjct: 8 ELNKKRHATKHFTDK-LVDPKDVRTAIEIATLAPSAHNSQPWK 49
>pdb|3CXU|A Chain A, Structure Of A Y149f Mutant Of Epoxide Hydrolase From
Solanum Tuberosum
pdb|3CXU|B Chain B, Structure Of A Y149f Mutant Of Epoxide Hydrolase From
Solanum Tuberosum
Length = 328
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 130 FATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYV 168
F +AL N+ + F+K NP + V+G+ I +Y+
Sbjct: 124 FRPDKVKALVNLSVHFSKRNPKMNVVEGLKAIFGEDHYI 162
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
0.319 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,745,871
Number of Sequences: 62578
Number of extensions: 216886
Number of successful extensions: 461
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 447
Number of HSP's gapped (non-prelim): 20
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)