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= 008800
(553 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 = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 56/222 (25%), Positives = 102/222 (45%), Gaps = 40/222 (18%)
Query: 352 KRIFYGGVDHKLRREVWAFLLGYYAYDSTYAEREYLRCIKKSEYENIKRQWQSISPEQAR 411
++I + G+ R VW L+GY ++ E R K+ EY + + + S + +R
Sbjct: 47 RQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQR--KRKEYRDSLKH--TFSDQHSR 102
Query: 412 RFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVHLLRDILLTYSFYNFDLGYCQGMSDL 471
+ + I+ D+ RT+ + + N L+ IL ++ + GY QG++DL
Sbjct: 103 DIPTWHQ----IEIDIPRTNPHIPLYQFKSVQNS--LQRILYLWAIRHPASGYVQGINDL 156
Query: 472 LSPIL--FVMED--------------------------ESQSFWCFVALMERLGPNFNRD 503
++P F+ E E+ +FWC L+E++ N+
Sbjct: 157 VTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHG 216
Query: 504 QNGMHSQLFALSKLVELLDNPLHNYFKQNDCLNYF-FCFRWV 544
Q G+ Q+ LS+LV+ +D L+N+F QN+ + + F FRW+
Sbjct: 217 QPGILRQVKNLSQLVKRIDADLYNHF-QNEHVEFIQFAFRWM 257
>pdb|1FKM|A Chain A, Crystal Structure Of The YptRAB-Gap Domain Of Gyp1p
Length = 396
Score = 66.2 bits (160), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 58/229 (25%), Positives = 105/229 (45%), Gaps = 41/229 (17%)
Query: 344 VMDSNALRKRIFYGGVDHKLRREVWAFLLGYYAYDSTYAEREYLRCIKKSEYENIKRQWQ 403
+++ LR+ I + G+ R VW L+GY ++ E R K+ EY + +
Sbjct: 20 IINQQDLRQ-ISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQR--KRKEYRDSLKH-- 74
Query: 404 SISPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVHLLRDILLTYSFYNFDLG 463
+ S + +R + + I+ D+ RT+ + + N L+ IL ++ + G
Sbjct: 75 TFSDQHSRDIPTWHQ----IEIDIPRTNPHIPLYQFKSVQNS--LQRILYLWAIRHPASG 128
Query: 464 YCQGMSDLLSPIL--FVMED--------------------------ESQSFWCFVALMER 495
Y QG++DL++P F+ E E+ +FWC L+E+
Sbjct: 129 YVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYXVDEQITDLEADTFWCLTKLLEQ 188
Query: 496 LGPNFNRDQNGMHSQLFALSKLVELLDNPLHNYFKQNDCLNYF-FCFRW 543
+ N+ Q G+ Q+ LS+LV+ +D L+N+F QN+ + + F FRW
Sbjct: 189 ITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHF-QNEHVEFIQFAFRW 236
>pdb|3DZX|A Chain A, Crystal Structure Of The Rabgap Domain Of Human Tbc1d22b
Length = 346
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 59/223 (26%), Positives = 100/223 (44%), Gaps = 35/223 (15%)
Query: 346 DSNALRKRIFYGGVDHKLRREVWAFLLGYYAYDSTYAEREYLRCIKKSEYENIKRQWQSI 405
D + LRK + GV ++R W L GY ++ + R K+ EY Q+
Sbjct: 40 DLDELRK-CSWPGVPREVRPITWRLLSGYLPANTERRKLTLQR--KREEYFGFIEQYYDS 96
Query: 406 SPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVH-LLRDILLTYSFYNFDLGY 464
E+ + T +R+ I D+ RT+ + F P V + IL ++ + GY
Sbjct: 97 RNEEHHQDT-YRQ----IHIDIPRTNPLIPLFQ---QPLVQEIFERILFIWAIRHPASGY 148
Query: 465 CQGMSDLLSPIL------FVMED-----------------ESQSFWCFVALMERLGPNFN 501
QG++DL++P +V ED E+ SFWC L++ + N+
Sbjct: 149 VQGINDLVTPFFVVFLSEYVEEDVENFDVTNLSQDMLRSIEADSFWCMSKLLDGIQDNYT 208
Query: 502 RDQNGMHSQLFALSKLVELLDNPLHNYFKQNDCLNYFFCFRWV 544
Q G+ ++ AL +LV +D +HN+F++ + F FRW+
Sbjct: 209 FAQPGIQKKVKALEELVSRIDEQVHNHFRRYEVEYLQFAFRWM 251
>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 = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 47/193 (24%), Positives = 76/193 (39%), Gaps = 28/193 (14%)
Query: 358 GVDHKLRREVWAFLLGYYAYDSTYAEREYLRCIKKSEYENIKRQWQSISPEQARRFTKFR 417
GV LR EVW L G +D+ Y I TK
Sbjct: 33 GVPEALRAEVWQLLAG--CHDNQAXLDRYRILI-----------------------TKDS 67
Query: 418 ERKGLIDKDVVRTDRSVTFFDGDDNPNVHLLRDILLTYSFYNFDLGYCQGMSDLLSPILF 477
++ +I +D+ RT + +F L I YS Y+ D+GYCQG S L+ +L
Sbjct: 68 AQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQS-FLAAVLL 126
Query: 478 VMEDESQSFWCFVALMERLGPN--FNRDQNGMHSQLFALSKLVELLDNPLHNYFKQNDCL 535
+ E Q+F V + G + + +H + + L +L + LH++F +
Sbjct: 127 LHXPEEQAFCVLVKIXYDYGLRDLYRNNFEDLHCKFYQLERLXQEQLPDLHSHFSDLNLE 186
Query: 536 NYFFCFRWVLIQF 548
+ + +W L F
Sbjct: 187 AHXYASQWFLTLF 199
>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 = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 55/245 (22%), Positives = 97/245 (39%), Gaps = 42/245 (17%)
Query: 330 GSEEWTTFLDN-----EGRVMDSNALRKRIFYGGVDHKLRREVWAFLLGYYAYDSTYAER 384
GSE + LD G D LR R+ + G+ +R W L GY +
Sbjct: 18 GSEREASRLDKFKQLLAGPNTDLEELR-RLSWSGIPKPVRPMTWKLLSGYLPANVDRRPA 76
Query: 385 EYLRCIKKSEYENIKRQWQSISPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPN 444
R K+ EY + ++ + T +R+ I D+ R P
Sbjct: 77 TLQR--KQKEYFAFIEHYYDSRNDEVHQDT-YRQ----IHIDIPRMSPEALIL----QPK 125
Query: 445 V-HLLRDILLTYSFYNFDLGYCQGMSDLLSP--ILFVME--------------------- 480
V + IL ++ + GY QG++DL++P ++F+ E
Sbjct: 126 VTEIFERILFIWAIRHPASGYVQGINDLVTPFFVVFICEYIEAEEVDTVDVSGVPAEVLC 185
Query: 481 -DESQSFWCFVALMERLGPNFNRDQNGMHSQLFALSKLVELLDNPLHNYFKQNDCLNYFF 539
E+ ++WC L++ + N+ Q G+ ++ L +LV +D +H + Q++ F
Sbjct: 186 NIEADTYWCMSKLLDGIQDNYTFAQPGIQMKVKMLEELVSRIDEQVHRHLDQHEVRYLQF 245
Query: 540 CFRWV 544
FRW+
Sbjct: 246 AFRWM 250
>pdb|3QYB|A Chain A, X-Ray Crystal Structure Of Human Tbc1d4 (As160) Rabgap
Domain
Length = 301
Score = 48.5 bits (114), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 34/125 (27%), Positives = 60/125 (48%), Gaps = 3/125 (2%)
Query: 426 DVVRTDRSVTFFDGDDNPNVHLLRDILLTYSFYNFDLGYCQGMSDLLSPILFVMEDESQS 485
D+ RT + +F P L ++L YS + ++GYCQG+S ++ +L + E Q+
Sbjct: 100 DLGRTFPTHPYFSVQLGPGQLSLFNLLKAYSLLDKEVGYCQGIS-FVAGVLLLHMSEEQA 158
Query: 486 FWCFVALMERLG--PNFNRDQNGMHSQLFALSKLVELLDNPLHNYFKQNDCLNYFFCFRW 543
F LM LG + D + Q++ LS+L+ L+N+ ++N+ + W
Sbjct: 159 FEMLKFLMYDLGFRKQYRPDMMSLQIQMYQLSRLLHDYHRDLYNHLEENEISPSLYAAPW 218
Query: 544 VLIQF 548
L F
Sbjct: 219 FLTLF 223
>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 = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 49/220 (22%), Positives = 88/220 (40%), Gaps = 24/220 (10%)
Query: 334 WTTFLDNEGRV---MDSNALRKRIFYGGVDHKLRREVWAFLLGYYAYDSTYAEREYLRCI 390
W L GR D + + G H R E+W FL + + ++
Sbjct: 33 WEKMLSTPGRSKIKFDMEKMHSAVGQGVPRHH-RGEIWKFLAEQFHLKHQFPSKQQ---P 88
Query: 391 KKSEYENIKRQWQSISPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVHLLRD 450
K Y+ + +Q S ++ I D+ RT + +F L +
Sbjct: 89 KDVPYKELLKQLTS--------------QQHAILIDLGRTFPTHPYFSAQLGAGQLSLYN 134
Query: 451 ILLTYSFYNFDLGYCQGMSDLLSPILFVMEDESQSFWCFVALMERLG--PNFNRDQNGMH 508
IL YS + ++GYCQG+S ++ IL + E ++F LM +G + D +
Sbjct: 135 ILKAYSLLDQEVGYCQGLS-FVAGILLLHMSEEEAFKMLKFLMFDMGLRKQYRPDMIILQ 193
Query: 509 SQLFALSKLVELLDNPLHNYFKQNDCLNYFFCFRWVLIQF 548
Q++ LS+L+ L+N+ ++++ + W L F
Sbjct: 194 IQMYQLSRLLHDYHRDLYNHLEEHEIGPSLYAAPWFLTMF 233
>pdb|2QQ8|A Chain A, Crystal Structure Of The Putative Rabgap Domain Of Human
Tbc1 Domain Family Member 14
Length = 334
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 50/210 (23%), Positives = 93/210 (44%), Gaps = 20/210 (9%)
Query: 352 KRIFYGGVDHKLRREVWAFLLGYYAYDSTYAEREYLRCIKKSEYENIKRQWQSISP---- 407
+ +++ G+ +R +VW+ +G + + C+ ++ K +W+S+S
Sbjct: 42 RDLWWQGIPPSVRGKVWSLAIGN---ELNITHELFDICLARA-----KERWRSLSTGGSE 93
Query: 408 ---EQARRFTKFRERK-GLIDKDVVRTDRSVTFFDGDDNPNVHLLRDILLTYSFYNFDLG 463
E A RE LI D+ RT ++ F P +L IL Y+ Y D+G
Sbjct: 94 VENEDAGFSAADREASLELIKLDISRTFPNLCIFQ-QGGPYHDMLHSILGAYTCYRPDVG 152
Query: 464 YCQGMSDLLSPILFVMEDESQSFWCFVALMER-LGPNFNRDQNGMHSQLFALSKLVELLD 522
Y QGMS ++ +L + D + +F F L+ + F R +G+ FA ++ +
Sbjct: 153 YVQGMS-FIAAVLILNLDTADAFIAFSNLLNKPCQMAFFRVDHGLMLTYFAAFEVFFEEN 211
Query: 523 NP-LHNYFKQNDCLNYFFCFRWVLIQFKRS 551
P L +FK+N+ + W+ + +S
Sbjct: 212 LPKLFAHFKKNNLTPDIYLIDWIFTLYSKS 241
>pdb|1GPD|G Chain G, Studies Of Asymmetry In The Three-Dimensional Structure Of
Lobster D- Glyceraldehyde-3-Phosphate Dehydrogenase
pdb|1GPD|R Chain R, Studies Of Asymmetry In The Three-Dimensional Structure Of
Lobster D- Glyceraldehyde-3-Phosphate Dehydrogenase
Length = 334
Score = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 387 LRCIKKSEYENIKRQWQSISPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVH 446
+R K+ Y++IK ++ S + F + E ++ D + +RS F D +
Sbjct: 244 VRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDD-VVSSDFIGDNRSSIF---DAKAGIQ 299
Query: 447 LLRDILLTYSFYNFDLGYCQGMSDLL 472
L + + S+Y+ + GY Q + DLL
Sbjct: 300 LSKTFVKVVSWYDNEFGYSQRVIDLL 325
>pdb|4GPD|1 Chain 1, The Structure Of Lobster Apo-D-Glyceraldehyde-3-Phosphate
Dehydrogenase At 3.0 Angstroms Resolution
pdb|4GPD|2 Chain 2, The Structure Of Lobster Apo-D-Glyceraldehyde-3-Phosphate
Dehydrogenase At 3.0 Angstroms Resolution
pdb|4GPD|3 Chain 3, The Structure Of Lobster Apo-D-Glyceraldehyde-3-Phosphate
Dehydrogenase At 3.0 Angstroms Resolution
pdb|4GPD|4 Chain 4, The Structure Of Lobster Apo-D-Glyceraldehyde-3-Phosphate
Dehydrogenase At 3.0 Angstroms Resolution
Length = 333
Score = 33.1 bits (74), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 387 LRCIKKSEYENIKRQWQSISPEQARRFTKFRERKGLIDKDVVRTDRSVTFFDGDDNPNVH 446
+R K+ Y++IK ++ S + F + E ++ D + +RS F D +
Sbjct: 243 VRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDD-VVSSDFIGDNRSSIF---DAKAGIQ 298
Query: 447 LLRDILLTYSFYNFDLGYCQGMSDLL 472
L + + S+Y+ + GY Q + DLL
Sbjct: 299 LSKTFVKVVSWYDNEFGYSQRVIDLL 324
>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
Polymerase
Length = 1193
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 460 FDLGYCQ---------GMSDLLSPILFVMEDESQSFWCFVALMERLGPNFNRDQNGMHSQ 510
F LG C L +P++ + E + F+ L+++ GP F N ++
Sbjct: 370 FSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYGPEFVTGYNIINFD 429
Query: 511 L-FALSKLVELLDNPLHNYFKQN 532
F L+KL ++ PL Y + N
Sbjct: 430 WPFLLAKLTDIYKVPLDGYGRMN 452
>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok
Length = 773
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 450 DILLTYSFYNFDLGYCQGMSDLLSPILFVMEDESQSFWCFVALMERLGPNFNRDQNG-MH 508
D+L+TY+ NFD Y + S++L + D S+ ++R+G F + G +H
Sbjct: 204 DVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEP------KIQRMGDRFAVEVKGRIH 257
Query: 509 SQLFAL 514
L+ +
Sbjct: 258 FDLYPV 263
>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
D.Tok. Deposition Of Second Native Structure At 2.4
Angstrom
Length = 733
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 450 DILLTYSFYNFDLGYCQGMSDLLSPILFVMEDESQSFWCFVALMERLGPNFNRDQNG-MH 508
D+L+TY+ NFD Y + S++L + D S+ ++R+G F + G +H
Sbjct: 204 DVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEP------KIQRMGDRFAVEVKGRIH 257
Query: 509 SQLFAL 514
L+ +
Sbjct: 258 FDLYPV 263
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
0.321 0.137 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,948,673
Number of Sequences: 62578
Number of extensions: 652769
Number of successful extensions: 1498
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1482
Number of HSP's gapped (non-prelim): 17
length of query: 553
length of database: 14,973,337
effective HSP length: 104
effective length of query: 449
effective length of database: 8,465,225
effective search space: 3800886025
effective search space used: 3800886025
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)