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= 005968
(667 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YK7|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst), In Complex With Cmp-3f-Neu5ac
Length = 326
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 96 MSSSSYYFDHLS--GSIRRAFNKRSIDDWDFDYSGFTTLQSNVEDKSKTAFGSDDFPVDD 153
+ SSSY D S G+I+R F + I DW + N D+ T F +DD
Sbjct: 123 IQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKT------RNASDEHYTIFKGLKNIMDD 176
Query: 154 EVRRKMTLVKDIEDALLLKTG 174
RRKMT + + DA LK G
Sbjct: 177 G-RRKMTYLP-LFDASELKAG 195
>pdb|2YK6|A Chain A, Structure Of Neisseria Los-Specific Sialyltransferase
(Nst), In Complex With Cdp
Length = 326
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 96 MSSSSYYFDHLS--GSIRRAFNKRSIDDWDFDYSGFTTLQSNVEDKSKTAFGSDDFPVDD 153
+ SSSY D S G+I+R F + I DW + N D+ T F +DD
Sbjct: 123 IQSSSYLGDEFSVNGTIKRNFARMMIGDWSIAKT------RNASDEHYTIFKGLKNIMDD 176
Query: 154 EVRRKMTLVKDIEDALLLKTG 174
RRKMT + + DA LK G
Sbjct: 177 G-RRKMTYLP-LFDASELKAG 195
>pdb|4DMV|A Chain A, Crystal Structure Of The Gt Domain Of Clostridium
Difficile Toxin A
pdb|4DMW|A Chain A, Crystal Structure Of The Gt Domain Of Clostridium
Difficile Toxin A (Tcda) In Complex With Udp And
Manganese
Length = 556
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 486 SELVRLAALYKYGGIYMDSDII 507
S++VRL AL +GG+Y+D D++
Sbjct: 283 SDIVRLLALKNFGGVYLDVDML 304
>pdb|3SRZ|A Chain A, Clostridium Difficile Toxin A (Tcda) Glucolsyltransferase
Domain Bound To Udp-Glucose
pdb|3SS1|A Chain A, Clostridium Difficile Toxin A (Tcda) Glucolsyltransferase
Domain
Length = 555
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 486 SELVRLAALYKYGGIYMDSDII 507
S++VRL AL +GG+Y+D D++
Sbjct: 268 SDIVRLLALKNFGGVYLDVDML 289
>pdb|2J7U|A Chain A, Dengue Virus Ns5 Rna Dependent Rna Polymerase Domain
pdb|2J7W|A Chain A, Dengue Virus Ns5 Rna Dependent Rna Polymerase Domain
Complexed With 3'dgtp
Length = 635
Score = 29.3 bits (64), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 24/39 (61%)
Query: 451 VAMPNLDELLKDTPAHEFASVWFEWRKTKFYNTHYSELV 489
+A+ ++ ++ KD P + + W +W++ F + H+ EL+
Sbjct: 414 LALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELI 452
>pdb|3VWS|A Chain A, Dengue Serotype 3 Rna-dependent Rna Polymerase Bound To
Nitd-107
pdb|4HHJ|A Chain A, Dengue Serotype 3 Rna-dependent Rna Polymerase
Length = 635
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 10/39 (25%), Positives = 24/39 (61%)
Query: 451 VAMPNLDELLKDTPAHEFASVWFEWRKTKFYNTHYSELV 489
+A+ ++ ++ KD P + + W +W++ F + H+ EL+
Sbjct: 414 LALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELI 452
>pdb|2VK9|A Chain A, Crystal Structure Of The Catalytic Domain Of Alpha-Toxin
From Clostridium Novyi
Length = 551
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 486 SELVRLAALYKYGGIYMDSDII 507
S+++R+A L KYGG+Y D D +
Sbjct: 267 SDILRIAILKKYGGVYCDLDFL 288
>pdb|1SUI|A Chain A, Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
pdb|1SUI|B Chain B, Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
pdb|1SUI|C Chain C, Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
pdb|1SUI|D Chain D, Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
pdb|1SUS|A Chain A, Crystal Structure Of Alfalfa Feruoyl Coenzyme A 3-O-
Methyltransferase
pdb|1SUS|B Chain B, Crystal Structure Of Alfalfa Feruoyl Coenzyme A 3-O-
Methyltransferase
pdb|1SUS|C Chain C, Crystal Structure Of Alfalfa Feruoyl Coenzyme A 3-O-
Methyltransferase
pdb|1SUS|D Chain D, Crystal Structure Of Alfalfa Feruoyl Coenzyme A 3-O-
Methyltransferase
Length = 247
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 447 FKVAVAMPNLDELLKDTPAH-EFASVWFEWRKTKFYNTHYSELVRLAALYKYGGI 500
F+ A+P LDE++KD H + ++ + K + N H RL L K GG+
Sbjct: 135 FREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHK----RLIDLVKVGGV 185
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 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,389,396
Number of Sequences: 62578
Number of extensions: 756555
Number of successful extensions: 1789
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1784
Number of HSP's gapped (non-prelim): 12
length of query: 667
length of database: 14,973,337
effective HSP length: 105
effective length of query: 562
effective length of database: 8,402,647
effective search space: 4722287614
effective search space used: 4722287614
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: 55 (25.8 bits)