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= 047609
(696 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 = 76.6 bits (187), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 42/157 (26%), Positives = 73/157 (46%), Gaps = 29/157 (18%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLF---------------------------- 462
+ IL ++A PA+GY QG++DL++PF F
Sbjct: 133 LQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDEQIT 192
Query: 463 EDNADAFWCFEMLLRRMRNNFQMEGPTGVMKQLEELWHILELTDREMYKHLSNIGAESLH 522
+ AD FWC LL ++ +N+ + G G+++Q++ L +++ D ++Y H N E +
Sbjct: 193 DLEADTFWCLTKLLEQITDNY-IHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQ 251
Query: 523 FAFRMLLVLFRRELSFNEALCMWEMMWAADYDEASAS 559
FAFR + L RE + MW+ + E ++S
Sbjct: 252 FAFRWMNCLLMREFQMGTVIRMWDTYLSETSQEVTSS 288
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 73.6 bits (179), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 71/157 (45%), Gaps = 29/157 (18%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLF---------------------------- 462
+ IL ++A PA+GY QG++DL++PF F
Sbjct: 113 LQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYXVDEQIT 172
Query: 463 EDNADAFWCFEMLLRRMRNNFQMEGPTGVMKQLEELWHILELTDREMYKHLSNIGAESLH 522
+ AD FWC LL ++ +N+ + G G+++Q++ L +++ D ++Y H N E +
Sbjct: 173 DLEADTFWCLTKLLEQITDNY-IHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQ 231
Query: 523 FAFRMLLVLFRRELSFNEALCMWEMMWAADYDEASAS 559
FAFR L RE + W+ + E ++S
Sbjct: 232 FAFRWXNCLLXREFQXGTVIRXWDTYLSETSQEVTSS 268
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 70.1 bits (170), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 42/136 (30%), Positives = 68/136 (50%), Gaps = 24/136 (17%)
Query: 434 ILAVYAWVDPATGYCQGMSDLLSPFVVLF------ED-----------------NADAFW 470
IL ++A PA+GY QG++DL++PF V+F ED AD+FW
Sbjct: 135 ILFIWAIRHPASGYVQGINDLVTPFFVVFLSEYVEEDVENFDVTNLSQDMLRSIEADSFW 194
Query: 471 CFEMLLRRMRNNFQMEGPTGVMKQLEELWHILELTDREMYKHLSNIGAESLHFAFRMLLV 530
C LL +++N+ P G+ K+++ L ++ D +++ H E L FAFR +
Sbjct: 195 CMSKLLDGIQDNYTFAQP-GIQKKVKALEELVSRIDEQVHNHFRRYEVEYLQFAFRWMNN 253
Query: 531 LFRRELSFNEALCMWE 546
L REL + +W+
Sbjct: 254 LLMRELPLRCTIRLWD 269
>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 = 63.5 bits (153), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 37/137 (27%), Positives = 65/137 (47%), Gaps = 25/137 (18%)
Query: 434 ILAVYAWVDPATGYCQGMSDLLSPFVVLF------------------------EDNADAF 469
IL ++A PA+GY QG++DL++PF V+F AD +
Sbjct: 133 ILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTY 192
Query: 470 WCFEMLLRRMRNNFQMEGPTGVMKQLEELWHILELTDREMYKHLSNIGAESLHFAFRMLL 529
WC LL +++N+ P G+ +++ L ++ D ++++HL L FAFR +
Sbjct: 193 WCMSKLLDGIQDNYTFAQP-GIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMN 251
Query: 530 VLFRRELSFNEALCMWE 546
L RE+ + +W+
Sbjct: 252 NLLMREVPLRCTIRLWD 268
>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 = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLFEDNADAFWCFEMLLRRMRNNFQMEGPTG 490
+ +IL Y+ +D GYCQG+S ++ ++L +AF + L+ M Q
Sbjct: 132 LYNILKAYSLLDQEVGYCQGLS-FVAGILLLHMSEEEAFKMLKFLMFDMGLRKQYRPDMI 190
Query: 491 VMK-QLEELWHILELTDREMYKHL 513
+++ Q+ +L +L R++Y HL
Sbjct: 191 ILQIQMYQLSRLLHDYHRDLYNHL 214
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLFEDNADAFWCFEMLLRR 478
+ IL Y P GY QGMS ++ ++L D ADAF F LL +
Sbjct: 137 LHSILGAYTCYRPDVGYVQGMS-FIAAVLILNLDTADAFIAFSNLLNK 183
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 50/111 (45%), Gaps = 6/111 (5%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLFEDNADAFWCFEMLLRRMRNNFQMEGPTG 490
+ ++L Y+ +D GYCQG+S ++ ++L AF + L+ + F+ +
Sbjct: 122 LFNLLKAYSLLDKEVGYCQGIS-FVAGVLLLHMSEEQAFEMLKFLMYDL--GFRKQYRPD 178
Query: 491 VMK---QLEELWHILELTDREMYKHLSNIGAESLHFAFRMLLVLFRRELSF 538
+M Q+ +L +L R++Y HL +A L LF + S
Sbjct: 179 MMSLQIQMYQLSRLLHDYHRDLYNHLEENEISPSLYAAPWFLTLFASQFSL 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 = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 49/108 (45%), Gaps = 12/108 (11%)
Query: 431 MSDILAVYAWVDPATGYCQGMSDLLSPFVVLFEDNADAFWC-----FEMLLRRM-RNNFQ 484
+ I Y+ D GYCQG S L+ ++L AF ++ LR + RNNF
Sbjct: 98 LYKICKAYSVYDEDIGYCQGQS-FLAAVLLLHXPEEQAFCVLVKIXYDYGLRDLYRNNF- 155
Query: 485 MEGPTGVMKQLEELWHILELTDREMYKHLSNIGAESLHFAFRMLLVLF 532
E QLE L +L D ++ H S++ E+ +A + L LF
Sbjct: 156 -EDLHCKFYQLERLXQE-QLPD--LHSHFSDLNLEAHXYASQWFLTLF 199
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 115 KALKLIVLGGVDPSIRPEVWEFLLGCY 141
K L +V GV ++R EVW+ L GC+
Sbjct: 24 KGLSTLVKSGVPEALRAEVWQLLAGCH 50
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
0.317 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,817,006
Number of Sequences: 62578
Number of extensions: 806529
Number of successful extensions: 1700
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: 1680
Number of HSP's gapped (non-prelim): 20
length of query: 696
length of database: 14,973,337
effective HSP length: 106
effective length of query: 590
effective length of database: 8,340,069
effective search space: 4920640710
effective search space used: 4920640710
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)