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= 009530
(532 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z2Z|A Chain A, Crystal Structure Of The Putative Trna Pseudouridine
Synthase D (Trud) From Methanosarcina Mazei, Northeast
Structural Genomics Target Mar1
pdb|1Z2Z|B Chain B, Crystal Structure Of The Putative Trna Pseudouridine
Synthase D (Trud) From Methanosarcina Mazei, Northeast
Structural Genomics Target Mar1
Length = 446
Score = 122 bits (307), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 84/257 (32%), Positives = 138/257 (53%), Gaps = 8/257 (3%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
GK+L L K + DT +S++L + + AGTKDKR+++TQ++++F AS++
Sbjct: 47 GKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTDASEIE 106
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGV---VVDSEDVIKASANS-LGRN 144
++ L I L ++ + LG L GN F IT+R + ++E ++K + + L +
Sbjct: 107 KIH--LKDIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDEILAQG 164
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKETD 203
G N+FG+QRFGS THLVG ++ G + K+A+ I +P E E AR++ K+T
Sbjct: 165 GVPNFFGIQRFGSVRPVTHLVGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQFVKDTL 224
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
D L+ P L ERA L P +Y + + +P+ L +VH YQS+++N
Sbjct: 225 DFKEGLKTYPLRLGHERAXXNHLIANPEDYSGSFRVLPQNLYRXFVHGYQSYIYNIILCR 284
Query: 264 RVQKH-GTEHVVVGDLV 279
R++ V GD+V
Sbjct: 285 RIEAGIPLNRAVEGDIV 301
>pdb|1SB7|A Chain A, Crystal Structure Of The E.Coli Pseudouridine Synthase
Trud
pdb|1SB7|B Chain B, Crystal Structure Of The E.Coli Pseudouridine Synthase
Trud
Length = 368
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 47/145 (32%), Positives = 72/145 (49%), Gaps = 8/145 (5%)
Query: 25 PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVT--VFKQ 82
P+ G+ + + K +T+ ++K L I R FAG KDK +V+ Q + V +
Sbjct: 56 PDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGK 115
Query: 83 RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
L+A +L G ++ ++ K L LG L GN FT+ LR V + D ++ +
Sbjct: 116 EXPDLSAF--QLEGCQVLEYARHKRKLRLGALKGNAFTLVLRE--VSNRDDVEQRLIDIC 171
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGA 167
G NYFG QRFG G ++L GA
Sbjct: 172 VKGVPNYFGAQRFGIGG--SNLQGA 194
>pdb|1SZW|A Chain A, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
Trud
pdb|1SZW|B Chain B, Crystal Structure Of E. Coli Trna Pseudouridine Synthase
Trud
Length = 379
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 47/145 (32%), Positives = 72/145 (49%), Gaps = 8/145 (5%)
Query: 25 PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVT--VFKQ 82
P+ G+ + + K +T+ ++K L I R FAG KDK +V+ Q + V +
Sbjct: 59 PDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGK 118
Query: 83 RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
L+A +L G ++ ++ K L LG L GN FT+ LR V + D ++ +
Sbjct: 119 EXPDLSAF--QLEGCQVLEYARHKRKLRLGALKGNAFTLVLRE--VSNRDDVEQRLIDIC 174
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGA 167
G NYFG QRFG G ++L GA
Sbjct: 175 VKGVPNYFGAQRFGIGG--SNLQGA 197
>pdb|1SI7|A Chain A, Structure Of E. Coli Trna Psi 13 Pseudouridine Synthase
Trud
Length = 369
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 47/145 (32%), Positives = 72/145 (49%), Gaps = 8/145 (5%)
Query: 25 PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVT--VFKQ 82
P+ G+ + + K +T+ ++K L I R FAG KDK +V+ Q + V +
Sbjct: 57 PDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGK 116
Query: 83 RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
L+A +L G ++ ++ K L LG L GN FT+ LR V + D ++ +
Sbjct: 117 EMPDLSAF--QLEGCQVLEYARHKRKLRLGALKGNAFTLVLRE--VSNRDDVEQRLIDIC 172
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGA 167
G NYFG QRFG G ++L GA
Sbjct: 173 VKGVPNYFGAQRFGIGG--SNLQGA 195
>pdb|3PSV|A Chain A, Structure Of E97d Mutant Of Tim From Plasmodium Falciparum
pdb|3PSV|B Chain B, Structure Of E97d Mutant Of Tim From Plasmodium Falciparum
Length = 248
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 7/114 (6%)
Query: 354 VIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYI 413
V++P V+ Y H + + + NV +F S TG K ++ E+ ++ +
Sbjct: 40 VVFP---VSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHF 96
Query: 414 DGNKPLAETDLDKIAK--AKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIK 465
D K ETD D K A L N +K VC + + + K E ++K +K
Sbjct: 97 DRRKYFHETDEDVREKLQASLKNNLK--AVVCFGESLEQREQNKTIEVITKQVK 148
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
0.316 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,012,943
Number of Sequences: 62578
Number of extensions: 685807
Number of successful extensions: 1562
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1540
Number of HSP's gapped (non-prelim): 31
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)