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= psy3106
(433 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3AFH|A Chain A, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With A Glutamyl-Amp
Analog
Length = 488
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%)
Query: 272 EVGDPLALRFEILDPNSPYEIFVRELVAMDGVDSSEIVLIDSNGCPTDHF 321
E G P+ ++F++L + +E ++ + D + +++ SNG PT +F
Sbjct: 152 EKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNF 201
>pdb|3AKZ|B Chain B, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|D Chain D, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|C Chain C, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
pdb|3AKZ|A Chain A, Crystal Structure Of Thermotoga Maritima Nondiscriminating
Glutamyl- Trna Synthetase In Complex With Trnagln And A
Glutamyl-Amp Analog
Length = 487
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%)
Query: 272 EVGDPLALRFEILDPNSPYEIFVRELVAMDGVDSSEIVLIDSNGCPTDHF 321
E G P+ ++F++L + +E ++ + D + +++ SNG PT +F
Sbjct: 151 EKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNF 200
>pdb|3AL0|C Chain C, Crystal Structure Of The Glutamine Transamidosome From
Thermotoga Maritima In The Glutamylation State
Length = 592
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 13/50 (26%), Positives = 28/50 (56%)
Query: 272 EVGDPLALRFEILDPNSPYEIFVRELVAMDGVDSSEIVLIDSNGCPTDHF 321
E G P+ ++F++L + +E ++ + D + +++ SNG PT +F
Sbjct: 256 EKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNF 305
>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 = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 207 IITSSDLGLAVTC---QYDLTNKTVSNEVDLGVQGDVKSALTEEVVVDSPNVAMKITDRS 263
+I D G+ T QY NK SN+ + D LT+EV+VD V M+I D +
Sbjct: 11 VIILGDSGVGKTSLMNQY--VNKKFSNQYKATIGADF---LTKEVMVDDRLVTMQIWDTA 65
Query: 264 GADVKPSAEV-----GDPLALRFEILDPNS 288
G + S V D L F++ PN+
Sbjct: 66 GQERFQSLGVAFYRGADCCVLVFDVTAPNT 95
>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 = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 207 IITSSDLGLAVTC---QYDLTNKTVSNEVDLGVQGDVKSALTEEVVVDSPNVAMKITDRS 263
+I D G+ T QY NK SN+ + D LT+EV+VD V M+I D +
Sbjct: 11 VIILGDSGVGKTSLMNQY--VNKKFSNQYKATIGADF---LTKEVMVDDRLVTMQIWDTA 65
Query: 264 GADVKPSAEV-----GDPLALRFEILDPNS 288
G + S V D L F++ PN+
Sbjct: 66 GQERFQSLGVAFYRGADCCVLVFDVTAPNT 95
>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 = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 207 IITSSDLGLAVTC---QYDLTNKTVSNEVDLGVQGDVKSALTEEVVVDSPNVAMKITDRS 263
+I D G+ T QY NK SN+ + D LT+EV+VD V M+I D +
Sbjct: 11 VIILGDSGVGKTSLMNQY--VNKKFSNQYKATIGADF---LTKEVMVDDRLVTMQIWDTA 65
Query: 264 GADVKPSAEV-----GDPLALRFEILDPNS 288
G + S V D L F++ PN+
Sbjct: 66 GQERFQSLGVAFYRGADCCVLVFDVTAPNT 95
>pdb|3NK3|A Chain A, Crystal Structure Of Full-Length Sperm Receptor Zp3 At 2.6
A Resolution
pdb|3NK3|B Chain B, Crystal Structure Of Full-Length Sperm Receptor Zp3 At 2.6
A Resolution
pdb|3NK4|A Chain A, Crystal Structure Of Full-Length Sperm Receptor Zp3 At 2.0
A Resolution
pdb|3NK4|B Chain B, Crystal Structure Of Full-Length Sperm Receptor Zp3 At 2.0
A Resolution
Length = 297
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 32/120 (26%), Positives = 53/120 (44%), Gaps = 12/120 (10%)
Query: 207 IITSSDLGLAVTCQYDLTNKTVSNEVDLGVQGDVKSALT-EEVVVDSPNVAMKITDRSGA 265
II ++ + + C Y + SN + SAL+ EE +V ++++ +
Sbjct: 90 IIRTNPAVIPIECHYPRREQVSSNAIR-PTWSPFNSALSAEERLV----FSLRLMSDDWS 144
Query: 266 DVKP--SAEVGDPLALRFEILDPNS-PYEIFVRELVAM---DGVDSSEIVLIDSNGCPTD 319
+P ++GD L ++ E+ N P +FV VA DG S +ID NGC D
Sbjct: 145 TERPFTGFQLGDILNIQAEVSTENHVPLRLFVDSCVAALSPDGDSSPHYAIIDFNGCLVD 204
>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 = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 207 IITSSDLGLAVTC---QYDLTNKTVSNEVDLGVQGDVKSALTEEVVVDSPNVAMKITDRS 263
+I D G+ T QY NK SN+ + D LT+EV+VD V M+I D +
Sbjct: 11 VIILGDSGVGKTSLMNQY--VNKKFSNQYKATIGADF---LTKEVMVDDRLVTMQIWDTA 65
Query: 264 GADVKPSAEV-----GDPLALRFEILDPNS 288
G + S V D L F++ PN+
Sbjct: 66 GLERFQSLGVAFYRGADCCVLVFDVTAPNT 95
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
0.320 0.136 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,334,528
Number of Sequences: 62578
Number of extensions: 508748
Number of successful extensions: 998
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 995
Number of HSP's gapped (non-prelim): 9
length of query: 433
length of database: 14,973,337
effective HSP length: 102
effective length of query: 331
effective length of database: 8,590,381
effective search space: 2843416111
effective search space used: 2843416111
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)