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= 021425
(312 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 69/217 (31%), Positives = 105/217 (48%), Gaps = 34/217 (15%)
Query: 75 GFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSN 134
GFL R E+ SL K + +Q +D QI+ D+ RT+P + + S
Sbjct: 79 GFLQRKR---KEYRDSL-KHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSV----- 129
Query: 135 QEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKS--------------DP-----DE 175
Q +L+ IL ++A +P YVQG+N+++ P + F + DP DE
Sbjct: 130 QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDE 189
Query: 176 EFSVSAEADTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEELWRHLEV 235
+ + EADTF+C +LL DN+ + GI + LSQL+K D +L+ H +
Sbjct: 190 QIT-DLEADTFWCLTKLLEQITDNYI----HGQPGILRQVKNLSQLVKRIDADLYNHFQN 244
Query: 236 TTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSD 272
QF AFRW+ LL +EF + +WDT LS+
Sbjct: 245 EHVEFIQF-AFRWMNCLLMREFQMGTVIRMWDTYLSE 280
>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 = 85.5 bits (210), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 76/287 (26%), Positives = 120/287 (41%), Gaps = 74/287 (25%)
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 FFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSDPDE------- 175
+ E + IL ++A +P YVQG+N+++ P + VF + E
Sbjct: 121 ILQPKVT------EIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTV 174
Query: 176 -------EFSVSAEADTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEE 228
E + EADT++C +LL G +DN+ + GI+ + L +L+ DE+
Sbjct: 175 DVSGVPAEVLCNIEADTYWCMSKLLDGIQDNYT----FAQPGIQMKVKMLEELVSRIDEQ 230
Query: 229 LWRHLEVTTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSDPDG 275
+ RHL+ QF AFRW+ LL +E ++ +WDT S+PDG
Sbjct: 231 VHRHLDQHEVRYLQF-AFRWMNNLLMREVPLRCTIRLWDTYQSEPDG 276
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 85.1 bits (209), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 79/286 (27%), Positives = 121/286 (42%), Gaps = 72/286 (25%)
Query: 3 GIPDGAGIRSTVWKLLLVYLPPDRGLWPSELAKKRSQYKHFKDDLLVNPSEITRRLDKST 62
G+P +R W+LL YLP + L +KR +Y F +
Sbjct: 51 GVP--REVRPITWRLLSGYLPANTERRKLTLQRKREEYFGFIEQY--------------- 93
Query: 63 IYESEEWKCESSGFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMH 122
+ SR+E H QD+ QI D+ RT+P +
Sbjct: 94 -------------YDSRNEEHH-----------------QDT--YRQIHIDIPRTNPLIP 121
Query: 123 FFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSDPDEE----FS 178
F QE + IL ++A +P YVQG+N+++ P + VF S+ EE F
Sbjct: 122 LFQQPLV-----QEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFLSEYVEEDVENFD 176
Query: 179 V---------SAEADTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEEL 229
V S EAD+F+C +LL G +DN+ + GI+ + L +L+ DE++
Sbjct: 177 VTNLSQDMLRSIEADSFWCMSKLLDGIQDNYT----FAQPGIQKKVKALEELVSRIDEQV 232
Query: 230 WRHLEVTTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSDPDG 275
H QF AFRW+ LL +E ++ +WDT S+P+G
Sbjct: 233 HNHFRRYEVEYLQF-AFRWMNNLLMRELPLRCTIRLWDTYQSEPEG 277
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 69/217 (31%), Positives = 103/217 (47%), Gaps = 34/217 (15%)
Query: 75 GFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSN 134
GFL R E+ SL K + +Q +D QI+ D+ RT+P + + S
Sbjct: 59 GFLQRKR---KEYRDSL-KHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSV----- 109
Query: 135 QEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKS--------------DP-----DE 175
Q +L+ IL ++A +P YVQG+N+++ P + F + DP DE
Sbjct: 110 QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYXVDE 169
Query: 176 EFSVSAEADTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEELWRHLEV 235
+ + EADTF+C +LL DN+ + GI + LSQL+K D +L+ H +
Sbjct: 170 QIT-DLEADTFWCLTKLLEQITDNYI----HGQPGILRQVKNLSQLVKRIDADLYNHFQN 224
Query: 236 TTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSD 272
QF AFRW LL +EF + WDT LS+
Sbjct: 225 EHVEFIQF-AFRWXNCLLXREFQXGTVIRXWDTYLSE 260
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 43/206 (20%), Positives = 83/206 (40%), Gaps = 20/206 (9%)
Query: 64 YESEEWKCESSGFLSRSEITHDEHPLSLGKSSIWNQFFQDSEIMEQIDRDVKRTHPDMHF 123
+ E WK + F + + + P + + Q + I D+ RT P +
Sbjct: 64 HRGEIWKFLAEQFHLKHQFPSKQQPKDVPYKELLKQL---TSQQHAILIDLGRTFPTHPY 120
Query: 124 FSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSDPDEEFSVSAEA 183
FS + Q +L NIL ++ L+ + Y QG++ + L + EA
Sbjct: 121 FSAQLG---AGQLSLYNILKAYSLLDQEVGYCQGLSFVAGILLLHMSEE---------EA 168
Query: 184 DTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEELWRHLEVTTKVNPQF 243
F+ G R +Q ++ ++ + +LS+LL ++ +L+ HLE ++ P
Sbjct: 169 FKMLKFLMFDMGLR----KQYRPDMIILQIQMYQLSRLLHDYHRDLYNHLE-EHEIGPSL 223
Query: 244 YAFRWITLLLTQEFNFADSLHIWDTL 269
YA W + +F ++D +
Sbjct: 224 YAAPWFLTMFASQFPLGFVARVFDMI 249
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 54/231 (23%), Positives = 88/231 (38%), Gaps = 41/231 (17%)
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 EQIDRDVKRTHPDMHFFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYY 167
E I D+ RT P++ F + + L +IL + P + YVQGM+ I A L
Sbjct: 111 ELIKLDISRTFPNLCIFQQGGPY----HDMLHSILGAYTCYRPDVGYVQGMSFIAAVLIL 166
Query: 168 VFKSDPDEEFSVSAEADTFFCFVELLSGFRDNFCQ----QLDNSVVGIRSTITRLSQLLK 223
+ AD F F LL + CQ ++D+ + + + +
Sbjct: 167 NLDT-----------ADAFIAFSNLL----NKPCQMAFFRVDHGL--MLTYFAAFEVFFE 209
Query: 224 EHDEELWRHLEVTTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSDPD 274
E+ +L+ H + + P Y WI L ++ + IWD D +
Sbjct: 210 ENLPKLFAHFK-KNNLTPDIYLIDWIFTLYSKSLPLDLACRIWDVFCRDGE 259
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 37/157 (23%), Positives = 73/157 (46%), Gaps = 17/157 (10%)
Query: 113 DVKRTHPDMHFFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEILAPLYYVFKSD 172
D+ RT P +FS Q +L N+L ++ L+ + Y QG++ + L +
Sbjct: 100 DLGRTFPTHPYFSVQLG---PGQLSLFNLLKAYSLLDKEVGYCQGISFVAGVL--LLHMS 154
Query: 173 PDEEFSVSAEADTFFCFVELLSGFRDNFCQQLDNSVVGIRSTITRLSQLLKEHDEELWRH 232
++ F + F +L GFR +Q ++ ++ + +LS+LL ++ +L+ H
Sbjct: 155 EEQAFEMLK-----FLMYDL--GFR----KQYRPDMMSLQIQMYQLSRLLHDYHRDLYNH 203
Query: 233 LEVTTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTL 269
LE +++P YA W L +F+ ++D +
Sbjct: 204 LE-ENEISPSLYAAPWFLTLFASQFSLGFVARVFDII 239
>pdb|3HZJ|A Chain A, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
pdb|3HZJ|B Chain B, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
pdb|3HZJ|C Chain C, Crystal Structure Of The Rabgap Domain Of The Rabgap1l
Protein
Length = 310
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 43/173 (24%), Positives = 67/173 (38%), Gaps = 21/173 (12%)
Query: 102 QDSEIMEQIDRDVKRTHPDMHFFSGDSSFATSNQEALKNILIVFAKLNPGIRYVQGMNEI 161
+DS I RD+ RT P +F QE+L I ++ + I Y QG + +
Sbjct: 65 KDSAQESVITRDIHRTFPAHDYFKDTGG---DGQESLYKICKAYSVYDEDIGYCQGQSFL 121
Query: 162 LAPLYYVFKSDPDEEFSVSAEADTFFCFVELLS--GFRDNFCQQLDNSVVGIRSTITRLS 219
A L P+E+ F V++ G RD + N+ + +L
Sbjct: 122 AAVL---LLHXPEEQ--------AFCVLVKIXYDYGLRDLY----RNNFEDLHCKFYQLE 166
Query: 220 QLLKEHDEELWRHLEVTTKVNPQFYAFRWITLLLTQEFNFADSLHIWDTLLSD 272
+L +E +L H + YA +W L T +F HI D LL +
Sbjct: 167 RLXQEQLPDLHSHFS-DLNLEAHXYASQWFLTLFTAKFPLCXVFHIIDLLLCE 218
>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 = 8.6, 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
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 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,104,674
Number of Sequences: 62578
Number of extensions: 352159
Number of successful extensions: 707
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 685
Number of HSP's gapped (non-prelim): 15
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
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: 51 (24.3 bits)