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= psy18019
(827 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 109 bits (272), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 79/287 (27%), Positives = 124/287 (43%), Gaps = 25/287 (8%)
Query: 360 WAKMFHKWDKVPADK---LKRRVYKGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQ 416
W ++ KW + L V G+P + R W N +D
Sbjct: 8 WGELLGKWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGC-------HDNQAXLD--- 57
Query: 417 RYEESTRKYEEMRDLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSV 476
RY R L K S I D++RT+ H+ F+D Q L+ + AYSV
Sbjct: 58 RY----------RILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSV 107
Query: 477 YNLEIGYCQGMSQIAAVLLMYLSEEEAFWALSSLVSDSKYSMHGFFIPGFPKLLRYQEHH 536
Y+ +IGYCQG S +AAVLL++ EE+AF L + D Y + + F L
Sbjct: 108 YDEDIGYCQGQSFLAAVLLLHXPEEQAFCVLVKIXYD--YGLRDLYRNNFEDLHCKFYQL 165
Query: 537 DKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDIYILEGERIMTA 596
+++ + LP L H N++ Y +WF F + P + D+ + EG I+
Sbjct: 166 ERLXQEQLPDLHSHFSDLNLEAHXYASQWFLTLFTAKFPLCXVFHIIDLLLCEGLNIIFH 225
Query: 597 MAYNLLKMHQRQLAKLSMDDILHFIQVKLEKQFQYTDDATIESLQKC 643
+A LLK + L + + L F +V+L K+++ ++A Q C
Sbjct: 226 VALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLXEQAC 272
Score = 67.4 bits (163), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 37/91 (40%), Positives = 51/91 (56%)
Query: 240 AAYSEMRDLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIG 299
A R L K S I D++RT+ H+ F+D Q L+ + AYSVY+ +IG
Sbjct: 54 AXLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIG 113
Query: 300 YCQGMSQIAAVLLMYLSEEEAFWALSSLVSD 330
YCQG S +AAVLL++ EE+AF L + D
Sbjct: 114 YCQGQSFLAAVLLLHXPEEQAFCVLVKIXYD 144
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 108 bits (271), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 73/254 (28%), Positives = 121/254 (47%), Gaps = 11/254 (4%)
Query: 374 KLKRRVYKGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQRYEESTRKYEEMRDLAW 433
K++ ++GIP S RG+ WS + ++R+ + E+ +
Sbjct: 40 KVRDLWWQGIPPSVRGKVWSLAIGNELNITHELFDICLARAKERWRSLSTGGSEVENEDA 99
Query: 434 KYSPDIRQ-----IDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMS 488
+S R+ I LD++RT+ +F+ + L ++L AY+ Y ++GY QGMS
Sbjct: 100 GFSAADREASLELIKLDISRTFPNLCIFQ-QGGPYHDMLHSILGAYTCYRPDVGYVQGMS 158
Query: 489 QIAAVLLMYLSEEEAFWALSSLVSDSKYSMHGFFIPGFPKLLRYQEHHDKIMSKFLPKLK 548
IAAVL++ L +AF A S+L++ K FF +L Y + + LPKL
Sbjct: 159 FIAAVLILNLDTADAFIAFSNLLN--KPCQMAFFRVDHGLMLTYFAAFEVFFEENLPKLF 216
Query: 549 KHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDIYILEGERIMTAMAYNLLKMHQRQ 608
H KNN+ IY + W F + +P L R+WD++ +GE + A +LK+ +
Sbjct: 217 AHFKKNNLTPDIYLIDWIFTLYSKSLPLDLACRIWDVFCRDGEEFLFRTALGILKLFEDI 276
Query: 609 LAKLSMDDILHFIQ 622
L K+ D +H Q
Sbjct: 277 LTKM---DFIHMAQ 287
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 256 IRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMSQIAAVLLMYL 315
+ I LD++RT+ +F+ + L ++L AY+ Y ++GY QGMS IAAVL++ L
Sbjct: 110 LELIKLDISRTFPNLCIFQ-QGGPYHDMLHSILGAYTCYRPDVGYVQGMSFIAAVLILNL 168
Query: 316 SEEEAFWALSSLVS 329
+AF A S+L++
Sbjct: 169 DTADAFIAFSNLLN 182
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 23/51 (45%)
Query: 82 SFFIPGFPKLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCF 132
+FF +L Y + + LPKL H KNN+ IY + W F +
Sbjct: 188 AFFRVDHGLMLTYFAAFEVFFEENLPKLFAHFKKNNLTPDIYLIDWIFTLY 238
>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 = 100 bits (248), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 67/258 (25%), Positives = 118/258 (45%), Gaps = 15/258 (5%)
Query: 369 KVPADKLKRRVYKGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQRYEESTRKYEEM 428
K +K+ V +G+P RG W S + D+
Sbjct: 46 KFDMEKMHSAVGQGVPRHHRGEIWKFLAEQFHLKHQFPSKQQPKDV------------PY 93
Query: 429 RDLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMS 488
++L + + I +D+ RT+ H F + Q L+N+L AYS+ + E+GYCQG+S
Sbjct: 94 KELLKQLTSQQHAILIDLGRTFPTHPYFSAQLGAGQLSLYNILKAYSLLDQEVGYCQGLS 153
Query: 489 QIAAVLLMYLSEEEAFWALSSLVSDSKYSMHGFFIPGFPKLLRYQEHHDKIMSKFLPKLK 548
+A +LL+++SEEEAF L L+ D + + P L +++ + L
Sbjct: 154 FVAGILLLHMSEEEAFKMLKFLMFD--MGLRKQYRPDMIILQIQMYQLSRLLHDYHRDLY 211
Query: 549 KHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDIYILEGERIMTAMAYNLLKMHQ-R 607
HL+++ + +Y WF F + P RV+D+ L+G ++ +A +LL H+
Sbjct: 212 NHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPL 271
Query: 608 QLAKLSMDDILHFIQVKL 625
L +++ I+ FI+ L
Sbjct: 272 ILQHENLETIVDFIKSTL 289
Score = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 53/85 (62%)
Query: 246 RDLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMS 305
++L + + I +D+ RT+ H F + Q L+N+L AYS+ + E+GYCQG+S
Sbjct: 94 KELLKQLTSQQHAILIDLGRTFPTHPYFSAQLGAGQLSLYNILKAYSLLDQEVGYCQGLS 153
Query: 306 QIAAVLLMYLSEEEAFWALSSLVSD 330
+A +LL+++SEEEAF L L+ D
Sbjct: 154 FVAGILLLHMSEEEAFKMLKFLMFD 178
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 63/243 (25%), Positives = 112/243 (46%), Gaps = 15/243 (6%)
Query: 381 KGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQRYEESTRKYEEMRDLAWKYSPDIR 440
+G+P S RG W + + D+ ++L + +
Sbjct: 48 EGVPKSRRGEIWQFLALQYRLRHRLPNKQQPPDI------------SYKELLKQLTAQQH 95
Query: 441 QIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMSQIAAVLLMYLSE 500
I +D+ RT+ H F + Q LFN+L AYS+ + E+GYCQG+S +A VLL+++SE
Sbjct: 96 AILVDLGRTFPTHPYFSVQLGPGQLSLFNLLKAYSLLDKEVGYCQGISFVAGVLLLHMSE 155
Query: 501 EEAFWALSSLVSDSKYSMHGFFIPGFPKLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGI 560
E+AF L L+ D + + P L +++ + L HL++N + +
Sbjct: 156 EQAFEMLKFLMYDLGFRKQ--YRPDMMSLQIQMYQLSRLLHDYHRDLYNHLEENEISPSL 213
Query: 561 YTLKWFFQCFLDRIPFKLTLRVWDIYILEGERIMTAMAYNLLKMHQRQLAKL-SMDDILH 619
Y WF F + RV+DI L+G ++ +A +LL + + + S ++I+
Sbjct: 214 YAAPWFLTLFASQFSLGFVARVFDIIFLQGTEVIFKVALSLLSSQETLIMECESFENIVE 273
Query: 620 FIQ 622
F++
Sbjct: 274 FLK 276
Score = 68.2 bits (165), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/85 (40%), Positives = 53/85 (62%)
Query: 246 RDLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMS 305
++L + + I +D+ RT+ H F + Q LFN+L AYS+ + E+GYCQG+S
Sbjct: 84 KELLKQLTAQQHAILVDLGRTFPTHPYFSVQLGPGQLSLFNLLKAYSLLDKEVGYCQGIS 143
Query: 306 QIAAVLLMYLSEEEAFWALSSLVSD 330
+A VLL+++SEE+AF L L+ D
Sbjct: 144 FVAGVLLLHMSEEQAFEMLKFLMYD 168
>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 = 50.1 bits (118), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 66/318 (20%), Positives = 128/318 (40%), Gaps = 48/318 (15%)
Query: 373 DKLKRRVYKGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQR-YEESTRKYEEMRDL 431
++L+R + GIP R W + P ++ +Q+ Y Y + R+
Sbjct: 41 EELRRLSWSGIPKPVRPMTWKLLSGYLPANV--DRRPATLQRKQKEYFAFIEHYYDSRND 98
Query: 432 AWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFN-VLAAYSVYNLEIGYCQGMSQI 490
+ RQI +D+ R E + + K T++F +L +++ + GY QG++ +
Sbjct: 99 E-VHQDTYRQIHIDIPRMSPEALILQP----KVTEIFERILFIWAIRHPASGYVQGINDL 153
Query: 491 AAVLLM-----YLSEEEA--------------------FWALSSLVSDSKYSMHGFFIPG 525
+ Y+ EE +W +S L+ D + F PG
Sbjct: 154 VTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLL-DGIQDNYTFAQPG 212
Query: 526 FPKLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDI 585
++ E +++S+ ++ +HLD++ V + +W + +P + T+R+WD
Sbjct: 213 IQMKVKMLE---ELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDT 269
Query: 586 YILEGERI----MTAMAYNLLKMHQRQLAKLSMDDILHFIQVKLEKQFQYTDDATIESLQ 641
Y E + + A L++ + L + ++L F+Q + DD I L
Sbjct: 270 YQSEPDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQ---NLPTAHWDDEDISLL- 325
Query: 642 KCLEELKRNKLDYAGQPS 659
L E R K +A P+
Sbjct: 326 --LAEAYRLKFAFADAPN 341
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 49/246 (19%), Positives = 102/246 (41%), Gaps = 38/246 (15%)
Query: 373 DKLKRRVYKGIPNSCRGRGWSXXXXXXXXXXXXESNPRSMDMRQRYEES---TRKYEEMR 429
D+L++ + G+P R W + R + ++++ EE +Y + R
Sbjct: 42 DELRKCSWPGVPREVRPITWRLLSGYLPA----NTERRKLTLQRKREEYFGFIEQYYDSR 97
Query: 430 DLAWKYSPDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMSQ 489
+ + RQI +D+ RT +F+ + Q +L +++ + GY QG++
Sbjct: 98 NEE-HHQDTYRQIHIDIPRTNPLIPLFQQ--PLVQEIFERILFIWAIRHPASGYVQGIND 154
Query: 490 IAA-VLLMYLSE-----------------------EEAFWALSSLVSDSKYSMHGFFIPG 525
+ +++LSE ++FW +S L+ D + F PG
Sbjct: 155 LVTPFFVVFLSEYVEEDVENFDVTNLSQDMLRSIEADSFWCMSKLL-DGIQDNYTFAQPG 213
Query: 526 FPKLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDI 585
K ++ E +++S+ ++ H + V+ + +W + +P + T+R+WD
Sbjct: 214 IQKKVKALE---ELVSRIDEQVHNHFRRYEVEYLQFAFRWMNNLLMRELPLRCTIRLWDT 270
Query: 586 YILEGE 591
Y E E
Sbjct: 271 YQSEPE 276
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 36/189 (19%), Positives = 74/189 (39%), Gaps = 35/189 (18%)
Query: 437 PDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMSQIAA---- 492
P QI++D+ RT +++ + Q L +L +++ + GY QG++ +
Sbjct: 105 PTWHQIEIDIPRTNPHIPLYQ--FKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFE 162
Query: 493 -VLLMYLS------------------------EEEAFWALSSLVSDSKYSMHGFFIPGFP 527
L YL E + FW L+ L+ + +I G P
Sbjct: 163 TFLTEYLPPSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLE----QITDNYIHGQP 218
Query: 528 KLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCFLDRIPFKLTLRVWDIYI 587
+LR ++ +++ + L H +V+ + +W + +R+WD Y+
Sbjct: 219 GILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYL 278
Query: 588 LEGERIMTA 596
E + +T+
Sbjct: 279 SETSQEVTS 287
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 39/190 (20%), Positives = 75/190 (39%), Gaps = 37/190 (19%)
Query: 437 PDIRQIDLDVNRTYREHNMFRDRYSVKQTQLFNVLAAYSVYNLEIGYCQGMSQIAA---- 492
P QI++D+ RT +++ + Q L +L +++ + GY QG++ +
Sbjct: 85 PTWHQIEIDIPRTNPHIPLYQ--FKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFE 142
Query: 493 -VLLMYLS------------------------EEEAFWALSSLVSDSKYSMHGFFIPGFP 527
L YL E + FW L+ L+ + +I G P
Sbjct: 143 TFLTEYLPPSQIDDVEIKDPSTYXVDEQITDLEADTFWCLTKLLE----QITDNYIHGQP 198
Query: 528 KLLRYQEHHDKIMSKFLPKLKKHLDKNNVDTGIYTLKWFFQCFLDR-IPFKLTLRVWDIY 586
+LR ++ +++ + L H +V+ + +W C L R +R WD Y
Sbjct: 199 GILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRW-XNCLLXREFQXGTVIRXWDTY 257
Query: 587 ILEGERIMTA 596
+ E + +T+
Sbjct: 258 LSETSQEVTS 267
>pdb|2RF4|B Chain B, Crystal Structure Of The Rna Polymerase I Subcomplex A1443
pdb|2RF4|D Chain D, Crystal Structure Of The Rna Polymerase I Subcomplex A1443
pdb|2RF4|F Chain F, Crystal Structure Of The Rna Polymerase I Subcomplex A1443
Length = 87
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 604 MHQRQLAK-LSMDDILHFIQVKLEKQFQYTDDATIESLQKCLEELKRNKLDYAGQPSPAE 662
+H QL + +S D++L F++ ++++ D T +L + +LKR + D+ G P +
Sbjct: 22 IHATQLPQHVSTDEVLQFLESFIDEKENIIDIDT--NLSSSISQLKRIQRDFKGLPPAQD 79
Query: 663 LPKSPLGV 670
+P+ V
Sbjct: 80 FSAAPIQV 87
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 0.135 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,586,487
Number of Sequences: 62578
Number of extensions: 1023916
Number of successful extensions: 2915
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2891
Number of HSP's gapped (non-prelim): 26
length of query: 827
length of database: 14,973,337
effective HSP length: 107
effective length of query: 720
effective length of database: 8,277,491
effective search space: 5959793520
effective search space used: 5959793520
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: 56 (26.2 bits)