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= 040788
(365 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 = 175 bits (444), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 96/255 (37%), Positives = 139/255 (54%), Gaps = 13/255 (5%)
Query: 56 WRKMIGVGGSDWKHYVRRKPHVVKRRIRKGIPDCLRGLVWQLISGSRDLLLMNPGVYEQ- 114
W +++G W + +P + ++ G+P+ LR VWQL++G D N ++
Sbjct: 8 WGELLG----KWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGCHD----NQAXLDRY 59
Query: 115 -LLIYETSTSELDIIRDISRTFPSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGYVQGMG 173
+LI + S E I RDI RTFP+H +F+ G GQ SLY + KAYSVYD D+GY QG
Sbjct: 60 RILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQS 119
Query: 174 FLAGLLLLYMSEEDAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLFQFDHLVKEHLPKL 233
FLA +LLL+ EE AF ++V K + LY+ + +Q + L +E LP L
Sbjct: 120 FLAAVLLLHXPEEQAFCVLV---KIXYDYGLRDLYRNNFEDLHCKFYQLERLXQEQLPDL 176
Query: 234 GEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIVFKVGLALLTYCHD 293
HF+ + YASQWF+T+F+ FP I D+ L EG+ I+F V LALL +
Sbjct: 177 HSHFSDLNLEAHXYASQWFLTLFTAKFPLCXVFHIIDLLLCEGLNIIFHVALALLKTSKE 236
Query: 294 DLIKLPFEKLIHALR 308
DL++ FE + R
Sbjct: 237 DLLQADFEGALKFFR 251
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 147 bits (372), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 83/259 (32%), Positives = 152/259 (58%), Gaps = 12/259 (4%)
Query: 82 IRKGIPDCLRGLVWQLISGSRDLL--LMN----PGVYEQLLIYETSTSELDIIRDISRTF 135
+++G+P RG +WQ ++ L L N P + + L+ + + + I+ D+ RTF
Sbjct: 46 LKEGVPKSRRGEIWQFLALQYRLRHRLPNKQQPPDISYKELLKQLTAQQHAILVDLGRTF 105
Query: 136 PSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGYVQGMGFLAGLLLLYMSEEDAFWLMVAL 195
P+H +F + GPGQ SL+N+LKAYS+ D++VGY QG+ F+AG+LLL+MSEE AF ++ L
Sbjct: 106 PTHPYFSVQLGPGQLSLFNLLKAYSLLDKEVGYCQGISFVAGVLLLHMSEEQAFEMLKFL 165
Query: 196 LKGAVHAPMEGLYQVGLPLVQQYLFQFDHLVKEHLPKLGEHFTKEMINPSMYASQWFITV 255
+ Y+ + +Q ++Q L+ ++ L H + I+PS+YA+ WF+T+
Sbjct: 166 M---YDLGFRKQYRPDMMSLQIQMYQLSRLLHDYHRDLYNHLEENEISPSLYAAPWFLTL 222
Query: 256 FSYSFPFHLALRIWDVFLFEGVKIVFKVGLALLTYCHDDLIKL-PFEKLIHALRN-FPE- 312
F+ F R++D+ +G +++FKV L+LL+ +++ FE ++ L+N P+
Sbjct: 223 FASQFSLGFVARVFDIIFLQGTEVIFKVALSLLSSQETLIMECESFENIVEFLKNTLPDM 282
Query: 313 DAMDPDKLLPVAYSIKVSK 331
+ + +K++ + + +SK
Sbjct: 283 NTSEMEKIITQVFEMDISK 301
>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 = 147 bits (370), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 83/240 (34%), Positives = 135/240 (56%), Gaps = 14/240 (5%)
Query: 56 WRKMIGVGGSDWKHYVRRKPHVVKRRIRKGIPDCLRGLVWQLISGSRDLLLMNPGV---- 111
W KM+ G + K H + +G+P RG +W+ ++ L P
Sbjct: 33 WEKMLSTPGRSKIKFDMEKMHSA---VGQGVPRHHRGEIWKFLAEQFHLKHQFPSKQQPK 89
Query: 112 ---YEQLLIYETSTSELDIIRDISRTFPSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGY 168
Y++LL TS I+ D+ RTFP+H +F + G GQ SLYN+LKAYS+ D++VGY
Sbjct: 90 DVPYKELLKQLTSQQH-AILIDLGRTFPTHPYFSAQLGAGQLSLYNILKAYSLLDQEVGY 148
Query: 169 VQGMGFLAGLLLLYMSEEDAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLFQFDHLVKE 228
QG+ F+AG+LLL+MSEE+AF ++ L+ + Y+ + ++Q ++Q L+ +
Sbjct: 149 CQGLSFVAGILLLHMSEEEAFKMLKFLM---FDMGLRKQYRPDMIILQIQMYQLSRLLHD 205
Query: 229 HLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIVFKVGLALL 288
+ L H + I PS+YA+ WF+T+F+ FP R++D+ +G +++FKV L+LL
Sbjct: 206 YHRDLYNHLEEHEIGPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLL 265
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 137 bits (346), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 95/284 (33%), Positives = 137/284 (48%), Gaps = 36/284 (12%)
Query: 78 VKRRIR----KGIPDCLRGLVWQLISGSR--------DLLLMNPGVYEQLLIYETSTSE- 124
R++R +GIP +RG VW L G+ D+ L E+ T SE
Sbjct: 37 CSRKVRDLWWQGIPPSVRGKVWSLAIGNELNITHELFDICLARAK--ERWRSLSTGGSEV 94
Query: 125 ---------------LDIIR-DISRTFPSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGY 168
L++I+ DISRTFP+ FQQ GP L+++L AY+ Y DVGY
Sbjct: 95 ENEDAGFSAADREASLELIKLDISRTFPNLCIFQQ-GGPYHDMLHSILGAYTCYRPDVGY 153
Query: 169 VQGMGFLAGLLLLYMSEEDAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLFQFDHLVKE 228
VQGM F+A +L+L + DAF LL ++V L+ Y F+ +E
Sbjct: 154 VQGMSFIAAVLILNLDTADAFIAFSNLLNKPCQM---AFFRVDHGLMLTYFAAFEVFFEE 210
Query: 229 HLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIVFKVGLALL 288
+LPKL HF K + P +Y W T++S S P LA RIWDVF +G + +F+ L +L
Sbjct: 211 NLPKLFAHFKKNNLTPDIYLIDWIFTLYSKSLPLDLACRIWDVFCRDGEEFLFRTALGIL 270
Query: 289 TYCHDDLIKLPFEKLIHALRNFPEDAMDPDKLLPVAYSIKVSKR 332
D L K+ F + L PED + ++L +I++ R
Sbjct: 271 KLFEDILTKMDFIHMAQFLTRLPED-LPAEELFASIATIQMQSR 313
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 67/292 (22%), Positives = 111/292 (38%), Gaps = 56/292 (19%)
Query: 85 GIPDCLRGLVWQLISG-------SRDLLLMNP-----GVYEQLLIYETSTSELDIIR--- 129
G+P +R + W+L+SG R L L G EQ D R
Sbjct: 51 GVPREVRPITWRLLSGYLPANTERRKLTLQRKREEYFGFIEQYYDSRNEEHHQDTYRQIH 110
Query: 130 -DISRTFPSHVFFQQRHGPGQRSLYN-VLKAYSVYDRDVGYVQGMG-----FLAGLLLLY 182
DI RT P FQQ P + ++ +L +++ GYVQG+ F L Y
Sbjct: 111 IDIPRTNPLIPLFQQ---PLVQEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFLSEY 167
Query: 183 MSEE-------------------DAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLFQFD 223
+ E+ D+FW M LL G ++ Y P +Q+ + +
Sbjct: 168 VEEDVENFDVTNLSQDMLRSIEADSFWCMSKLLDG-----IQDNYTFAQPGIQKKVKALE 222
Query: 224 HLVKEHLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKI---- 279
LV ++ HF + + +A +W + P +R+WD + E
Sbjct: 223 ELVSRIDEQVHNHFRRYEVEYLQFAFRWMNNLLMRELPLRCTIRLWDTYQSEPEGFSHFH 282
Query: 280 VFKVGLALLTYCHDDLIKLPFEKLIHALRNFPEDAMDPDK---LLPVAYSIK 328
++ L+ + + L + F+ L+ L+N P ++ LL AY +K
Sbjct: 283 LYVCAAFLIKWRKEILDEEDFQGLLMLLQNLPTIHWGNEEIGLLLAEAYRLK 334
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 63/302 (20%), Positives = 111/302 (36%), Gaps = 58/302 (19%)
Query: 78 VKRRIRKGIPDCLRGLVWQLISG------SRDLLLMNPGVYEQLLI----YETSTSEL-- 125
++R GIP +R + W+L+SG R + E Y++ E+
Sbjct: 43 LRRLSWSGIPKPVRPMTWKLLSGYLPANVDRRPATLQRKQKEYFAFIEHYYDSRNDEVHQ 102
Query: 126 DIIR----DISRTFPSHVFFQQRHGPGQRSLYN-VLKAYSVYDRDVGYVQGMG-----FL 175
D R DI R P + Q P ++ +L +++ GYVQG+ F
Sbjct: 103 DTYRQIHIDIPRMSPEALILQ----PKVTEIFERILFIWAIRHPASGYVQGINDLVTPFF 158
Query: 176 AGLLLLYMSEE--------------------DAFWLMVALLKGAVHAPMEGLYQVGLPLV 215
+ Y+ E D +W M LL G ++ Y P +
Sbjct: 159 VVFICEYIEAEEVDTVDVSGVPAEVLCNIEADTYWCMSKLLDG-----IQDNYTFAQPGI 213
Query: 216 QQYLFQFDHLVKEHLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFE 275
Q + + LV ++ H + + +A +W + P +R+WD + E
Sbjct: 214 QMKVKMLEELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMREVPLRCTIRLWDTYQSE 273
Query: 276 GVKI----VFKVGLALLTYCHDDLIKLPFEKLIHALRNFPE---DAMDPDKLLPVAYSIK 328
++ L+ + + L + F++L+ L+N P D D LL AY +K
Sbjct: 274 PDGFSHFHLYVCAAFLVRWRKEILEEKDFQELLLFLQNLPTAHWDDEDISLLLAEAYRLK 333
Query: 329 VS 330
+
Sbjct: 334 FA 335
>pdb|2G77|A Chain A, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 410
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 43/180 (23%), Positives = 64/180 (35%), Gaps = 36/180 (20%)
Query: 130 DISRTFPSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGYVQGMG-----FLAGLLLLYMS 184
DI RT P +Q + Q SL +L +++ GYVQG+ F L Y+
Sbjct: 113 DIPRTNPHIPLYQFKSV--QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLP 170
Query: 185 ------------------------EEDAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLF 220
E D FW + LL+ Y G P + + +
Sbjct: 171 PSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDN-----YIHGQPGILRQVK 225
Query: 221 QFDHLVKEHLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIV 280
LVK L HF E + +A +W + F +R+WD +L E + V
Sbjct: 226 NLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQEV 285
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 43/180 (23%), Positives = 64/180 (35%), Gaps = 36/180 (20%)
Query: 130 DISRTFPSHVFFQQRHGPGQRSLYNVLKAYSVYDRDVGYVQGMG-----FLAGLLLLYMS 184
DI RT P +Q + Q SL +L +++ GYVQG+ F L Y+
Sbjct: 93 DIPRTNPHIPLYQFKSV--QNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLP 150
Query: 185 ------------------------EEDAFWLMVALLKGAVHAPMEGLYQVGLPLVQQYLF 220
E D FW + LL+ + Y G P + + +
Sbjct: 151 PSQIDDVEIKDPSTYXVDEQITDLEADTFWCLTKLLEQ-----ITDNYIHGQPGILRQVK 205
Query: 221 QFDHLVKEHLPKLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIV 280
LVK L HF E + +A +W + F +R WD +L E + V
Sbjct: 206 NLSQLVKRIDADLYNHFQNEHVEFIQFAFRWXNCLLXREFQXGTVIRXWDTYLSETSQEV 265
>pdb|3QWL|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 7
Length = 294
Score = 32.0 bits (71), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 1/86 (1%)
Query: 232 KLGEHFTKEMINPSMYASQWFITVFSYSFPFHLALRIWDVFLFEGVKIVFKVGLALLTYC 291
+L H P + WF F+ P R+WD + KI+ V + +L
Sbjct: 188 RLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILVFVAVEILLTF 247
Query: 292 HDDLIKL-PFEKLIHALRNFPEDAMD 316
++ L EK+ L N P+D+ D
Sbjct: 248 KIKVMALNSAEKITKFLENIPQDSSD 273
>pdb|3U0H|A Chain A, The Structure Of A Xylose Isomerase Domain Protein From
Alicyclobacillus Acidocaldarius Subsp. Acidocaldarius.
pdb|3U0H|B Chain B, The Structure Of A Xylose Isomerase Domain Protein From
Alicyclobacillus Acidocaldarius Subsp. Acidocaldarius
Length = 281
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 293 DDLIKLPFEKLIHA----LRNFPEDAMDPDKLLP 322
DDL +LP EK+++ R+ PEDA D +LLP
Sbjct: 191 DDLAQLPPEKVVYVHINDTRDAPEDAHDGKRLLP 224
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
0.324 0.141 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,273,087
Number of Sequences: 62578
Number of extensions: 470181
Number of successful extensions: 1193
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1169
Number of HSP's gapped (non-prelim): 16
length of query: 365
length of database: 14,973,337
effective HSP length: 100
effective length of query: 265
effective length of database: 8,715,537
effective search space: 2309617305
effective search space used: 2309617305
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)