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= psy9524
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LLU|A Chain A, Crystal Structure Of The Nucleotide-Binding Domain Of Ras-
Related Gtp-Binding Protein C
Length = 196
Score = 122 bits (307), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 58/80 (72%), Positives = 67/80 (83%), Gaps = 2/80 (2%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQD- 59
MGLRRSGK+SIQKVVF KMSPNETLFLE TNK+ K+DI+NSSF+ +Q+WD PGQMDF D
Sbjct: 26 MGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQMDFFDP 85
Query: 60 -FDAELIFARCGALIFVIDT 78
FD E+IF GALI+VID
Sbjct: 86 TFDYEMIFRGTGALIYVIDA 105
>pdb|2Q3F|A Chain A, X-Ray Crystal Structure Of Putative Human Ras-Related
Gtp Binding D In Complex With Gmppnp
pdb|2Q3F|B Chain B, X-Ray Crystal Structure Of Putative Human Ras-Related
Gtp Binding D In Complex With Gmppnp
Length = 181
Score = 116 bits (290), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 55/79 (69%), Positives = 65/79 (82%), Gaps = 2/79 (2%)
Query: 2 GLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQD-- 59
GLRRSGK+SIQKVVF K SPNETLFLE TNK+ +ED++NSSF+ +Q+WD PGQ+DF D
Sbjct: 11 GLRRSGKSSIQKVVFHKXSPNETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPT 70
Query: 60 FDAELIFARCGALIFVIDT 78
FD E IF GALIFVID+
Sbjct: 71 FDYEXIFRGTGALIFVIDS 89
>pdb|4ARZ|B Chain B, The Crystal Structure Of Gtr1p-Gtr2p Complexed With
Gtp-Gdp
Length = 341
Score = 64.7 bits (156), Expect = 1e-11, Method: Composition-based stats.
Identities = 33/80 (41%), Positives = 52/80 (65%), Gaps = 4/80 (5%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDF--Q 58
MG+RR GK+SI KVVF M P +TL+LE T+ + E S+ + + + PGQ+++
Sbjct: 15 MGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHF--STLIDLAVMELPGQLNYFEP 72
Query: 59 DFDAELIFARCGALIFVIDT 78
+D+E +F GAL++VID+
Sbjct: 73 SYDSERLFKSVGALVYVIDS 92
>pdb|3R7W|B Chain B, Crystal Structure Of Gtr1p-Gtr2p Complex
pdb|3R7W|D Chain D, Crystal Structure Of Gtr1p-Gtr2p Complex
Length = 331
Score = 60.8 bits (146), Expect = 2e-10, Method: Composition-based stats.
Identities = 31/79 (39%), Positives = 50/79 (63%), Gaps = 4/79 (5%)
Query: 2 GLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDF--QD 59
G+RR GK+SI KVVF P +TL+LE T+ + E S+ + + + PGQ+++
Sbjct: 6 GVRRCGKSSICKVVFHNXQPLDTLYLESTSNPSLEHF--STLIDLAVXELPGQLNYFEPS 63
Query: 60 FDAELIFARCGALIFVIDT 78
+D+E +F GAL++VID+
Sbjct: 64 YDSERLFKSVGALVYVIDS 82
>pdb|1VG1|A Chain A, Gdp-bound Rab7
pdb|1VG9|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|D Chain D, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|F Chain F, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
pdb|1VG9|H Chain H, The Crystal Structures Of The Rep-1 Protein In Complex
With C-Terminally Truncated Rab7 Protein
Length = 185
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 7 GKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFDAELIF 66
GKTS+ K N+ G + +TKE + + + Q+WD GQ FQ
Sbjct: 20 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYR 79
Query: 67 -ARCGALIF 74
A C L+F
Sbjct: 80 GADCCVLVF 88
>pdb|3LAW|A Chain A, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|B Chain B, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|C Chain C, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|D Chain D, Structure Of Gtp-Bound L129f Mutant Rab7
pdb|3LAW|E Chain E, Structure Of Gtp-Bound L129f Mutant Rab7
Length = 207
Score = 32.3 bits (72), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 7 GKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFDAELIF 66
GKTS+ K N+ G + +TKE + + + Q+WD GQ FQ
Sbjct: 20 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYR 79
Query: 67 -ARCGALIF 74
A C L+F
Sbjct: 80 GADCCVLVF 88
>pdb|1VG0|B Chain B, The Crystal Structures Of The Rep-1 Protein In Complex
With Monoprenylated Rab7 Protein
pdb|1VG8|A Chain A, Gppnhp-Bound Rab7
pdb|1VG8|B Chain B, Gppnhp-Bound Rab7
pdb|1VG8|C Chain C, Gppnhp-Bound Rab7
pdb|1VG8|D Chain D, Gppnhp-Bound Rab7
Length = 207
Score = 32.3 bits (72), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 7 GKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFDAELIF 66
GKTS+ K N+ G + +TKE + + + Q+WD GQ FQ
Sbjct: 20 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYR 79
Query: 67 -ARCGALIF 74
A C L+F
Sbjct: 80 GADCCVLVF 88
>pdb|4ARZ|A Chain A, The Crystal Structure Of Gtr1p-Gtr2p Complexed With
Gtp-Gdp
Length = 310
Score = 32.3 bits (72), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDF 60
MG SGK+S++ ++F S +T L T + + + LWDC GQ F +
Sbjct: 12 MGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLGNMTLNLWDCGGQDVFMEN 71
Query: 61 ----DAELIFARCGALIFVIDT 78
+ IF LI V D
Sbjct: 72 YFTKQKDHIFQMVQVLIHVFDV 93
>pdb|1T91|A Chain A, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|B Chain B, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|C Chain C, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1T91|D Chain D, Crystal Structure Of Human Small Gtpase Rab7(Gtp)
pdb|1YHN|A Chain A, Structure Basis Of Rilp Recruitment By Rab7
Length = 207
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 1/69 (1%)
Query: 7 GKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFDAELIF 66
GKTS+ K N+ G + +TKE + + + Q+WD G FQ
Sbjct: 20 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGLERFQSLGVAFYR 79
Query: 67 -ARCGALIF 74
A C L+F
Sbjct: 80 GADCCVLVF 88
>pdb|1QGI|A Chain A, Chitosanase From Bacillus Circulans
Length = 259
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 3 LRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFDA 62
L RSG +S +K + TL ++ TNK K + Q+ G+M+ ++ D+
Sbjct: 190 LARSGSSSNEKTFMKNFHAKRTLVVD-TNKYNKPPNGKNRVKQWDTLVDMGKMNLKNVDS 248
Query: 63 EL 64
E+
Sbjct: 249 EI 250
>pdb|1Z06|A Chain A, Gppnhp-Bound Rab33 Gtpase
Length = 189
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 44 LQYQLWDCPGQMDFQDFDAELIFARCGALIFVIDTS 79
++ QLWD GQ F+ + + A++FV D +
Sbjct: 69 IKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMT 104
>pdb|2G77|B Chain B, Crystal Structure Of Gyp1 Tbc Domain In Complex With Rab33
Gtpase Bound To Gdp And Alf3
Length = 198
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 44 LQYQLWDCPGQMDFQDFDAELIFARCGALIFVIDTS 79
++ QLWD GQ F+ + + A++FV D +
Sbjct: 78 IKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDXT 113
>pdb|3C6L|A Chain A, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
Complexed With Mouse Tcr 2w20
pdb|3C6L|E Chain E, Crystal Structure Of Mouse Mhc Class Ii I-Ab3K PEPTIDE
Complexed With Mouse Tcr 2w20
Length = 185
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 16 FQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMD-----FQDFDAEL 64
F S N F +GT + K +I N YQL D P D F DFD+++
Sbjct: 88 FCAASDNRIFFGDGTQLVVKPNIQNPEPAVYQLKD-PRSQDSTLCLFTDFDSQI 140
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
0.323 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,156,354
Number of Sequences: 62578
Number of extensions: 67285
Number of successful extensions: 182
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 167
Number of HSP's gapped (non-prelim): 15
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)