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= 043646
(625 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T3I|A Chain A, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
pdb|1T3I|B Chain B, Structure Of Slr0077SUFS, THE ESSENTIAL CYSTEINE
Desulfurase From Synechocystis Pcc 6803
Length = 420
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 45/214 (21%), Positives = 85/214 (39%), Gaps = 23/214 (10%)
Query: 78 LTYADHTASGRSLRYIEDYIINNVLPFYGNTHTSDSYVGQRMTKMVHEASNYIKRCLGGG 137
L Y D+ A+ + R + + +++ N H + R T N + + +
Sbjct: 29 LVYLDNAATSQKPRAVLEKLMHYYENDNANVHRGAHQLSVRATDAYEAVRNKVAKFINAR 88
Query: 138 QADAIIFCGAGTTAAIKRLQEVMGITVPSIMRDKLITSLRDEERWVVFLGPYEHHSNLLS 197
I++ T AI + G+ D++IT++ EHHSNL+
Sbjct: 89 SPREIVYT-RNATEAINLVAYSWGMNNLK-AGDEIITTVM------------EHHSNLVP 134
Query: 198 WRQSLAEVVEI----GLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTR 253
W+ A+ + LD+ D+E ++ L +++ L + SN G +
Sbjct: 135 WQMVAAKTGAVLKFVQLDEQESFDLEHFKTLL-----SEKTKLVTVVHISNTLGCVNPAE 189
Query: 254 SIARLLHQYGGFACFDFAASGPYVKINLRSRNID 287
IA+L HQ G D S P+ ++++ + D
Sbjct: 190 EIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCD 223
>pdb|1C0N|A Chain A, Csdb Protein, Nifs Homologue
Length = 406
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 55/110 (50%), Gaps = 9/110 (8%)
Query: 184 VFLGPYEHHSNLLSWRQSL----AEVVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSF 239
+ + EHH+N++ W+ AE+ I L+ +G L +E L + L+ AA R L +
Sbjct: 116 IIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPT---LFDAATR--LLAI 170
Query: 240 SACSNVTGIYSDTRSIARLLHQYGGFACFDFAASGPYVKINLRSRNIDGY 289
+ SNV G + + L HQ+G D A + + +++++ + D Y
Sbjct: 171 THVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFY 220
>pdb|1KMJ|A Chain A, E. Coli NifsCSDB PROTEIN AT 2.0A WITH THE CYSTEINE
PERSULFIDE Intermediate (Residue Css).
pdb|1KMK|A Chain A, E. Coli NifsCSDB PROTEIN AT 2.20A WITH THE CYSTEINE
PERSELENIDE Intermediate (Residue Csz)
Length = 406
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 53/110 (48%), Gaps = 9/110 (8%)
Query: 184 VFLGPYEHHSNLLSWRQSL----AEVVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSF 239
+ + EHH+N++ W+ AE+ I L+ +G L +E L + + ++ L +
Sbjct: 116 IIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFD-----EKTRLLAI 170
Query: 240 SACSNVTGIYSDTRSIARLLHQYGGFACFDFAASGPYVKINLRSRNIDGY 289
+ SNV G + + L HQ+G D A + + +++++ + D Y
Sbjct: 171 THVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFY 220
>pdb|1I29|A Chain A, Crystal Structure Of Csdb Complexed With
L-Propargylglycine
Length = 406
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 53/110 (48%), Gaps = 9/110 (8%)
Query: 184 VFLGPYEHHSNLLSWRQSL----AEVVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSF 239
+ + EHH+N++ W+ AE+ I L+ +G L +E L + + ++ L +
Sbjct: 116 IIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFD-----EKTRLLAI 170
Query: 240 SACSNVTGIYSDTRSIARLLHQYGGFACFDFAASGPYVKINLRSRNIDGY 289
+ SNV G + + L HQ+G D A + + +++++ + D Y
Sbjct: 171 THVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFY 220
>pdb|1JF9|A Chain A, Crystal Structure Of Selenocysteine Lyase
Length = 408
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 53/110 (48%), Gaps = 9/110 (8%)
Query: 184 VFLGPYEHHSNLLSWRQSL----AEVVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSF 239
+ + EHH+N++ W+ AE+ I L+ +G L +E L + + ++ L +
Sbjct: 118 IIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFD-----EKTRLLAI 172
Query: 240 SACSNVTGIYSDTRSIARLLHQYGGFACFDFAASGPYVKINLRSRNIDGY 289
+ SNV G + + L HQ+G D A + + +++++ + D Y
Sbjct: 173 THVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFY 222
>pdb|3CAI|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rv3778c
Protein
pdb|3CAI|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Rv3778c
Protein
Length = 406
Score = 35.4 bits (80), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 231 AKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGGFACFDFAASGPYVKINLRSRNID 287
+K L + ++ S G +D R++ +L+H G D +A+ PY +++R + D
Sbjct: 163 SKSTRLVAVNSASGTLGGVTDLRAMTKLVHDVGALVVVDHSAAAPYRLLDIRETDAD 219
>pdb|1HBQ|A Chain A, Crystal Structure Of Liganded And Unliganded Forms Of
Bovine Plasma Retinol-Binding Protein
Length = 183
Score = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 205 VVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGG 264
V E +D+NG Q+ + +L ++ C+++ G ++DT A+ +Y G
Sbjct: 42 VAEFSVDENG---------QMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWG 92
Query: 265 FACF 268
A F
Sbjct: 93 VASF 96
>pdb|1AQB|A Chain A, Retinol-Binding Protein (Rbp) From Pig Plasma
Length = 183
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 205 VVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGG 264
V E +D+NG + A + +L ++ C+++ G ++DT A+ +Y G
Sbjct: 42 VAEFSVDENGHMSATA---------KGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWG 92
Query: 265 FACF 268
A F
Sbjct: 93 VASF 96
>pdb|1KT5|A Chain A, Crystal Structure Of Bovine Holo-rbp At Ph 4.0
Length = 175
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 205 VVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGG 264
V E +D+NG + A + +L ++ C+++ G ++DT A+ +Y G
Sbjct: 42 VAEFSVDENGHMSATA---------KGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWG 92
Query: 265 FACF 268
A F
Sbjct: 93 VASF 96
>pdb|1KT3|A Chain A, Crystal Structure Of Bovine Holo-Rbp At Ph 2.0
pdb|1KT4|A Chain A, Crystal Structure Of Bovine Holo-Rbp At Ph 3.0
pdb|1KT6|A Chain A, Crystal Structure Of Bovine Holo-Rbp At Ph 9.0
pdb|1KT7|A Chain A, Crystal Structure Of Bovine Holo-rbp At Ph 7.0
pdb|1ERB|A Chain A, The Interaction Of N-Ethyl Retinamide With Plasma Retinol-
Binding Protein (Rbp) And The Crystal Structure Of The
Retinoid-Rbp Complex At 1.9 Angstroms Resolution
pdb|1FEL|A Chain A, Crystallographic Studies On Complexes Between Retinoids
And Plasma Retinol-Binding Protein
pdb|1FEM|A Chain A, Crystallographic Studies On Complexes Between Retinoids
And Plasma Retinol-Binding Protein
pdb|1FEN|A Chain A, Crystallographic Studies On Complexes Between Retinoids
And Plasma Retinol-Binding Protein
pdb|1HBP|A Chain A, Crystal Structure Of Liganded And Unliganded Forms Of
Bovine Plasma Retinol-Binding Protein
Length = 183
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 205 VVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGG 264
V E +D+NG + A + +L ++ C+++ G ++DT A+ +Y G
Sbjct: 42 VAEFSVDENGHMSATA---------KGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWG 92
Query: 265 FACF 268
A F
Sbjct: 93 VASF 96
>pdb|1RLB|E Chain E, Retinol Binding Protein Complexed With Transthyretin
pdb|1RLB|F Chain F, Retinol Binding Protein Complexed With Transthyretin
Length = 174
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 205 VVEIGLDDNGLLDIEALRSQLELYKAAKRPMLGSFSACSNVTGIYSDTRSIARLLHQYGG 264
V E +D+NG + A + +L ++ C+++ G ++DT A+ +Y G
Sbjct: 42 VAEFSVDENGHMSATA---------KGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWG 92
Query: 265 FACF 268
A F
Sbjct: 93 VASF 96
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 0.137 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,439,754
Number of Sequences: 62578
Number of extensions: 680401
Number of successful extensions: 1539
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1531
Number of HSP's gapped (non-prelim): 15
length of query: 625
length of database: 14,973,337
effective HSP length: 105
effective length of query: 520
effective length of database: 8,402,647
effective search space: 4369376440
effective search space used: 4369376440
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: 54 (25.4 bits)