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= 019449
(341 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 = 72.4 bits (176), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 44/170 (25%), Positives = 77/170 (45%), Gaps = 30/170 (17%)
Query: 169 HQIGLDVVRTDRSLVFYESETNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMI------ 222
HQI +D+ RT+ + Y+ ++ Q L +L +++ GYVQG+ND+ +P
Sbjct: 108 HQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTE 167
Query: 223 ----------------------VLLENEADAFWCFEHTMRRLRENFRTNTGMIGVQSQLS 260
+ + EAD FWC + ++ +N+ G G+ Q+
Sbjct: 168 YLPPSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIH--GQPGILRQVK 225
Query: 261 TLSQIIRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSFVDALYLWE 310
LSQ+++ ID L+ H ++ FAFR + L REF + +W+
Sbjct: 226 NLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWD 275
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 44/170 (25%), Positives = 75/170 (44%), Gaps = 30/170 (17%)
Query: 169 HQIGLDVVRTDRSLVFYESETNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMI------ 222
HQI +D+ RT+ + Y+ ++ Q L +L +++ GYVQG+ND+ +P
Sbjct: 88 HQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTE 147
Query: 223 ----------------------VLLENEADAFWCFEHTMRRLRENFRTNTGMIGVQSQLS 260
+ + EAD FWC + ++ +N+ G G+ Q+
Sbjct: 148 YLPPSQIDDVEIKDPSTYXVDEQITDLEADTFWCLTKLLEQITDNYIH--GQPGILRQVK 205
Query: 261 TLSQIIRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSFVDALYLWE 310
LSQ+++ ID L+ H ++ FAFR L REF + W+
Sbjct: 206 NLSQLVKRIDADLYNHFQNEHVEFIQFAFRWXNCLLXREFQXGTVIRXWD 255
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 64.7 bits (156), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 42/164 (25%), Positives = 74/164 (45%), Gaps = 25/164 (15%)
Query: 170 QIGLDVVRTDRSLVFYESETNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMIVL----- 224
QI +D+ RT+ + ++ Q +L I++ GYVQG+ND+ +P V+
Sbjct: 108 QIHIDIPRTNPLIPLFQQPLVQEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFLSEY 167
Query: 225 ----LEN--------------EADAFWCFEHTMRRLRENFRTNTGMIGVQSQLSTLSQII 266
+EN EAD+FWC + +++N+ G+Q ++ L +++
Sbjct: 168 VEEDVENFDVTNLSQDMLRSIEADSFWCMSKLLDGIQDNY--TFAQPGIQKKVKALEELV 225
Query: 267 RTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSFVDALYLWE 310
ID ++H H + FAFR + L RE + LW+
Sbjct: 226 SRIDEQVHNHFRRYEVEYLQFAFRWMNNLLMRELPLRCTIRLWD 269
>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 = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 75/138 (54%), Gaps = 7/138 (5%)
Query: 169 HQIGLDVVRTDRSLVFYESE--TNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMIVLLE 226
H I +D+ RT + ++ ++ Q L+++L YS +D ++GY QG++ + +++L
Sbjct: 105 HAILIDLGRTFPTHPYFSAQLGAGQLSLYNILKAYSLLDQEVGYCQGLSFVAG-ILLLHM 163
Query: 227 NEADAFWCFEHTM--RRLRENFRTNTGMIGVQSQLSTLSQIIRTIDPKLHQHLEDLDGGE 284
+E +AF + M LR+ +R + MI +Q Q+ LS+++ L+ HLE+ + G
Sbjct: 164 SEEEAFKMLKFLMFDMGLRKQYRPD--MIILQIQMYQLSRLLHDYHRDLYNHLEEHEIGP 221
Query: 285 YLFAFRMLMVLFRREFSF 302
L+A + +F +F
Sbjct: 222 SLYAAPWFLTMFASQFPL 239
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 71/165 (43%), Gaps = 27/165 (16%)
Query: 170 QIGLDVVRTDRSLVFYESETNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMIV------ 223
QI +D+ R + + + + +L I++ GYVQG+ND+ +P V
Sbjct: 107 QIHIDIPRMSPEALILQPKVTEI-FERILFIWAIRHPASGYVQGINDLVTPFFVVFICEY 165
Query: 224 ------------------LLENEADAFWCFEHTMRRLRENFRTNTGMIGVQSQLSTLSQI 265
L EAD +WC + +++N+ G+Q ++ L ++
Sbjct: 166 IEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLLDGIQDNY--TFAQPGIQMKVKMLEEL 223
Query: 266 IRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSFVDALYLWE 310
+ ID ++H+HL+ + FAFR + L RE + LW+
Sbjct: 224 VSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWD 268
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 81/152 (53%), Gaps = 8/152 (5%)
Query: 156 ISDKKVLQWMLGL-HQIGLDVVRTDRSLVFYESE--TNQAKLWDVLAIYSWVDNDIGYVQ 212
IS K++L+ + H I +D+ RT + ++ + Q L+++L YS +D ++GY Q
Sbjct: 81 ISYKELLKQLTAQQHAILVDLGRTFPTHPYFSVQLGPGQLSLFNLLKAYSLLDKEVGYCQ 140
Query: 213 GMNDICSPMIVLLENEADAFWCFEHTMRRL--RENFRTNTGMIGVQSQLSTLSQIIRTID 270
G++ + +++L +E AF + M L R+ +R + M+ +Q Q+ LS+++
Sbjct: 141 GISFVAG-VLLLHMSEEQAFEMLKFLMYDLGFRKQYRPD--MMSLQIQMYQLSRLLHDYH 197
Query: 271 PKLHQHLEDLDGGEYLFAFRMLMVLFRREFSF 302
L+ HLE+ + L+A + LF +FS
Sbjct: 198 RDLYNHLEENEISPSLYAAPWFLTLFASQFSL 229
>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 = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 31/129 (24%), Positives = 59/129 (45%), Gaps = 15/129 (11%)
Query: 191 QAKLWDVLAIYSWVDNDIGYVQGMNDICSPMIVLLENEADAFWC------FEHTMRRL-R 243
Q L+ + YS D DIGY QG + + + ++LL + +C +++ +R L R
Sbjct: 95 QESLYKICKAYSVYDEDIGYCQGQSFLAA--VLLLHXPEEQAFCVLVKIXYDYGLRDLYR 152
Query: 244 ENFRTNTGMIGVQSQLSTLSQIIRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSFV 303
NF + + L ++ + P LH H DL+ + +A + + LF +F
Sbjct: 153 NNFE------DLHCKFYQLERLXQEQLPDLHSHFSDLNLEAHXYASQWFLTLFTAKFPLC 206
Query: 304 DALYLWEIL 312
++ ++L
Sbjct: 207 XVFHIIDLL 215
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 67/150 (44%), Gaps = 6/150 (4%)
Query: 167 GLHQIGLDVVRTDRSL-VFYESETNQAKLWDVLAIYSWVDNDIGYVQGMNDICSPMIVLL 225
L I LD+ RT +L +F + L +L Y+ D+GYVQGM+ I + +I+ L
Sbjct: 109 SLELIKLDISRTFPNLCIFQQGGPYHDMLHSILGAYTCYRPDVGYVQGMSFIAAVLILNL 168
Query: 226 ENEADAFWCFEHTMRRLREN--FRTNTGMIGVQSQLSTLSQIIRTIDPKLHQHLEDLDGG 283
+ ADAF F + + + + FR + G++ + + PKL H + +
Sbjct: 169 DT-ADAFIAFSNLLNKPCQMAFFRVDHGLM--LTYFAAFEVFFEENLPKLFAHFKKNNLT 225
Query: 284 EYLFAFRMLMVLFRREFSFVDALYLWEILA 313
++ + L+ + A +W++
Sbjct: 226 PDIYLIDWIFTLYSKSLPLDLACRIWDVFC 255
>pdb|2IS9|A Chain A, Structure Of Yeast Dcn-1
Length = 204
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 243 RENFRTNTGMIGVQSQLSTLSQIIRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSF 302
RE+F + M G S +S + + I+T+D KLH+ L+ Y +AF +++ R++
Sbjct: 62 REDFLSTWFMQGC-STISDMQECIKTLDVKLHEDLQYFTQI-YNYAFNLILDPNRKDIDT 119
Query: 303 VDALYLWEIL 312
+ + W++
Sbjct: 120 DEGIQYWKLF 129
>pdb|3O2P|A Chain A, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb)
pdb|3O6B|A Chain A, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|C Chain C, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|E Chain E, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|G Chain G, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|I Chain I, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3TDI|B Chain B, Yeast Cul1whb-Dcn1p Acetylated Ubc12n Complex
pdb|3TDI|A Chain A, Yeast Cul1whb-Dcn1p Acetylated Ubc12n Complex
Length = 202
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 243 RENFRTNTGMIGVQSQLSTLSQIIRTIDPKLHQHLEDLDGGEYLFAFRMLMVLFRREFSF 302
RE+F + M G S +S + + I+T+D KLH+ L+ Y +AF +++ R++
Sbjct: 60 REDFLSTWFMQGC-STISDMQECIKTLDVKLHEDLQYF-TQIYNYAFNLILDPNRKDIDT 117
Query: 303 VDALYLWEIL 312
+ + W++
Sbjct: 118 DEGIQYWKLF 127
>pdb|2OKC|A Chain A, Crystal Structure Of Type I Restriction Enzyme Stysji M
Protein (np_813429.1) From Bacteroides Thetaiotaomicron
Vpi-5482 At 2.20 A Resolution
pdb|2OKC|B Chain B, Crystal Structure Of Type I Restriction Enzyme Stysji M
Protein (np_813429.1) From Bacteroides Thetaiotaomicron
Vpi-5482 At 2.20 A Resolution
Length = 445
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 118 PIIGSGKFITAAIVTDDGQSLQDSNRDSL-DQGWH-VDGAISDKKVLQWMLGLHQIGLDV 175
P G+G F+ A GQS RD L D+ H VD + L LH IG
Sbjct: 178 PACGTGGFLLTAYDYXKGQSASKEKRDFLRDKALHGVDNTPLVVTLASXNLYLHGIG--- 234
Query: 176 VRTDRSLVFYES--ETNQAKLWDVL 198
TDRS + E E + L DV+
Sbjct: 235 --TDRSPIVCEDSLEKEPSTLVDVI 257
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
0.323 0.139 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,830,604
Number of Sequences: 62578
Number of extensions: 391690
Number of successful extensions: 852
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 829
Number of HSP's gapped (non-prelim): 22
length of query: 341
length of database: 14,973,337
effective HSP length: 100
effective length of query: 241
effective length of database: 8,715,537
effective search space: 2100444417
effective search space used: 2100444417
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)