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= 003745
(798 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 = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 39/136 (28%), Positives = 59/136 (43%), Gaps = 34/136 (25%)
Query: 32 RGVKWRINLGILPSSYSSIED-LRRVTADSRRRYAEIRRHLLVDPHWHKDGSNSPDLVMD 90
R V W++ +G LP + E L+R R+ Y + +H D H S D+
Sbjct: 39 RPVVWKLLIGYLPVNTKRQEGFLQR----KRKEYRDSLKHTFSDQH-------SRDI--- 84
Query: 91 NPLSQNPDSTWGRFFRSAELEKMVDQDLSRLYPEHGSYFQTPGCQGMLRRILLLWCLRHP 150
TW + ++ D+ R P H +Q Q L+RIL LW +RHP
Sbjct: 85 --------PTWHQ----------IEIDIPRTNP-HIPLYQFKSVQNSLQRILYLWAIRHP 125
Query: 151 EFGYRQGMHELLAPLL 166
GY QG+++L+ P
Sbjct: 126 ASGYVQGINDLVTPFF 141
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 29/66 (43%)
Query: 302 VIEASSAMYHLLSVADSSLHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFA 361
++ + L+ D+ L++H VE F RW L REF G ++ WD +
Sbjct: 200 ILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWXNCLLXREFQXGTVIRXWDTYLS 259
Query: 362 SDSSKV 367
S +V
Sbjct: 260 ETSQEV 265
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 39/136 (28%), Positives = 59/136 (43%), Gaps = 34/136 (25%)
Query: 32 RGVKWRINLGILPSSYSSIED-LRRVTADSRRRYAEIRRHLLVDPHWHKDGSNSPDLVMD 90
R V W++ +G LP + E L+R R+ Y + +H D H S D+
Sbjct: 59 RPVVWKLLIGYLPVNTKRQEGFLQR----KRKEYRDSLKHTFSDQH-------SRDI--- 104
Query: 91 NPLSQNPDSTWGRFFRSAELEKMVDQDLSRLYPEHGSYFQTPGCQGMLRRILLLWCLRHP 150
TW + ++ D+ R P H +Q Q L+RIL LW +RHP
Sbjct: 105 --------PTWHQ----------IEIDIPRTNP-HIPLYQFKSVQNSLQRILYLWAIRHP 145
Query: 151 EFGYRQGMHELLAPLL 166
GY QG+++L+ P
Sbjct: 146 ASGYVQGINDLVTPFF 161
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 302 VIEASSAMYHLLSVADSSLHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFA 361
++ + L+ D+ L++H VE F RW+ L REF +G ++ +WD +
Sbjct: 220 ILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLS 279
Query: 362 SDSSKV 367
S +V
Sbjct: 280 ETSQEV 285
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 52/119 (43%), Gaps = 31/119 (26%)
Query: 129 FQTPGCQGMLRRILLLWCLRHPEFGYRQGMHELLAPLLYVL----------HVDVERLSQ 178
FQ P Q + RIL +W +RHP GY QG+++L+ P V + DV LSQ
Sbjct: 123 FQQPLVQEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFLSEYVEEDVENFDVTNLSQ 182
Query: 179 --VRNEHEDHFTDKFDGLSFHENDLTYNFDFKKFLDSMEDE--IGSHGNSVKVRSVDEL 233
+R+ D F + K LD ++D G KV++++EL
Sbjct: 183 DMLRSIEADSF-----------------WCMSKLLDGIQDNYTFAQPGIQKKVKALEEL 224
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 16/97 (16%)
Query: 262 MEHDAYCMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEAS-SAMYHLLSVADSSL 320
+E D++ L+ G Q + + A P I+ A+ L+S D +
Sbjct: 188 IEADSFWCMSKLLDGIQDNYTFAQ---------------PGIQKKVKALEELVSRIDEQV 232
Query: 321 HSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWD 357
H+H VE F RW+ L RE L + +WD
Sbjct: 233 HNHFRRYEVEYLQFAFRWMNNLLMRELPLRCTIRLWD 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 = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 112 KMVDQDLSRLYPEHGSYFQTPGCQGMLRRILLLWCLRHPEFGYRQGMHELLAPLLYVL-- 169
+ + D+ R+ PE + P + RIL +W +RHP GY QG+++L+ P V
Sbjct: 106 RQIHIDIPRMSPE--ALILQPKVTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFIC 163
Query: 170 -HVDVERLSQV 179
+++ E + V
Sbjct: 164 EYIEAEEVDTV 174
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 37/97 (38%), Gaps = 16/97 (16%)
Query: 262 MEHDAYCMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEASSAMYH-LLSVADSSL 320
+E D Y L+ G Q + + A P I+ M L+S D +
Sbjct: 187 IEADTYWCMSKLLDGIQDNYTFAQ---------------PGIQMKVKMLEELVSRIDEQV 231
Query: 321 HSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWD 357
H HL + V F RW+ L RE L + +WD
Sbjct: 232 HRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWD 268
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 320 LHSHLVELGVEPQYFGLRWLRVLFGREFSLGDLLIIWDEIFASDSSKVNK 369
L++HL E + P + W LF +FSLG + ++D IF + + K
Sbjct: 200 LYNHLEENEISPSLYAAPWFLTLFASQFSLGFVARVFDIIFLQGTEVIFK 249
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 33.5 bits (75), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 95 QNPDSTWGRFFRSAELEKMVDQDLSRLYPEHGSYFQTPGCQGMLRRILLLWCLRHPEFGY 154
+N D+ + R A LE ++ D+SR +P + Q ML IL + P+ GY
Sbjct: 95 ENEDAGFSAADREASLE-LIKLDISRTFPNLCIFQQGGPYHDMLHSILGAYTCYRPDVGY 153
Query: 155 RQGMHELLAPLLYVLHVD 172
QGM + A L +L++D
Sbjct: 154 VQGMSFIAAVL--ILNLD 169
>pdb|3NK6|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
pdb|3NK6|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
pdb|3NK7|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
S-Adenosyl- L-Methionine Complex
pdb|3NK7|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
S-Adenosyl- L-Methionine Complex
Length = 277
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 20/26 (76%)
Query: 531 SDPTPRTVDNGTKHSRSSIRRSLLED 556
SDP + + + TKHSR+SI+ +L+ED
Sbjct: 14 SDPAVQRIIDVTKHSRASIKTTLIED 39
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 8/67 (11%)
Query: 208 KKFLDSMEDEIGSHGNSVKVRSVDELDPEIQTIVQLSDAYG-----AEGELGIVLSEKFM 262
KK L+ ++ + + ++S+ E+ P I+T+VQL +YG A+ E I+ F
Sbjct: 313 KKLLEKLKTDYFTRSPEQHLKSLAEMKPVIETLVQLVISYGKRFEAAKQEKSII---DFS 369
Query: 263 EHDAYCM 269
+ + YC+
Sbjct: 370 DLEHYCL 376
>pdb|4HLQ|A Chain A, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|C Chain C, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|E Chain E, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|G Chain G, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
pdb|4HLQ|I Chain I, Crystal Structure Of Human Rab1b Bound To Gdp And Bef3 In
Complex With The Gap Domain Of Tbc1d20 From Homo Sapiens
Length = 305
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 34/159 (21%), Positives = 64/159 (40%), Gaps = 39/159 (24%)
Query: 148 RHPEFGYRQGMHELLAPLLYVLHVDVERLSQVRNEHEDHFTDKFDGLSFHENDLTYNFDF 207
R+P+ Y QG H+++ L V+ ERL+ T + LS H
Sbjct: 136 RNPQLHYYQGYHDIVVTFLLVVG---ERLA----------TSLVEKLSTHH--------L 174
Query: 208 KKFLDSMEDEIGSHGNSVKVRSVDELDPEIQTIVQLSDAYGAEGELGIVLSEKFMEHDAY 267
+ F+D D H + + +D+++PE+ +Q E+G + + ++
Sbjct: 175 RDFMDPTMDNT-KHILNYLMPIIDQVNPELHDFMQ-------SAEVGTIFALSWL----I 222
Query: 268 CMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEAS 306
F ++ + V + DFF H L+P+ A+
Sbjct: 223 TWFGHVLSDFRHVVRLYDFFLACHP------LMPIYFAA 255
>pdb|4HL4|A Chain A, Crystal Structure Of The Human Tbc1d20 Rabgap Domain
Length = 292
Score = 29.3 bits (64), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 34/159 (21%), Positives = 64/159 (40%), Gaps = 39/159 (24%)
Query: 148 RHPEFGYRQGMHELLAPLLYVLHVDVERLSQVRNEHEDHFTDKFDGLSFHENDLTYNFDF 207
R+P+ Y QG H+++ L V+ ERL+ T + LS H
Sbjct: 123 RNPQLHYYQGYHDIVVTFLLVVG---ERLA----------TSLVEKLSTHH--------L 161
Query: 208 KKFLDSMEDEIGSHGNSVKVRSVDELDPEIQTIVQLSDAYGAEGELGIVLSEKFMEHDAY 267
+ F+D D H + + +D+++PE+ +Q E+G + + ++
Sbjct: 162 RDFMDPTMDN-TKHILNYLMPIIDQVNPELHDFMQ-------SAEVGTIFALSWL----I 209
Query: 268 CMFDALMVGSQGSVSMADFFAHSHADGSLTCLLPVIEAS 306
F ++ + V + DFF H L+P+ A+
Sbjct: 210 TWFGHVLSDFRHVVRLYDFFLACHP------LMPIYFAA 242
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
0.314 0.131 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,460,598
Number of Sequences: 62578
Number of extensions: 910339
Number of successful extensions: 1482
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1466
Number of HSP's gapped (non-prelim): 19
length of query: 798
length of database: 14,973,337
effective HSP length: 107
effective length of query: 691
effective length of database: 8,277,491
effective search space: 5719746281
effective search space used: 5719746281
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)