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= 026438
(238 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FE7|A Chain A, Structure Of Xylose-binding Transcription Activator Xylr
Length = 412
Score = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 32/115 (27%), Positives = 52/115 (45%), Gaps = 27/115 (23%)
Query: 103 RVALSSSCSKDAERNISEPPNQ--QASQTSVKMPTQQSSGISSPWAVDDFLQFSDFESSG 160
R+ L + +K +R + E + QASQ S W D F++ DF +
Sbjct: 27 RITLLFNANKAYDRQVVEGVGEYLQASQ--------------SEW--DIFIE-EDFRARI 69
Query: 161 KKEQLEFGELEWIADMGI--FNDQLPQEALAAAEVPQLPVSQSNNLISSYRPTKF 213
K + +W+ D I F+D+ ++ALA +VP + V S +L SY P +
Sbjct: 70 DKIK------DWLGDGVIADFDDKQIEQALADVDVPIVGVGGSYHLAESYPPVHY 118
>pdb|4FE4|A Chain A, Crystal Structure Of Apo E. Coli Xylr
pdb|4FE4|B Chain B, Crystal Structure Of Apo E. Coli Xylr
pdb|4FE4|C Chain C, Crystal Structure Of Apo E. Coli Xylr
Length = 392
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 32/115 (27%), Positives = 52/115 (45%), Gaps = 27/115 (23%)
Query: 103 RVALSSSCSKDAERNISEPPNQ--QASQTSVKMPTQQSSGISSPWAVDDFLQFSDFESSG 160
R+ L + +K +R + E + QASQ S W D F++ DF +
Sbjct: 7 RITLLFNANKAYDRQVVEGVGEYLQASQ--------------SEW--DIFIE-EDFRARI 49
Query: 161 KKEQLEFGELEWIADMGI--FNDQLPQEALAAAEVPQLPVSQSNNLISSYRPTKF 213
K + +W+ D I F+D+ ++ALA +VP + V S +L SY P +
Sbjct: 50 DKIK------DWLGDGVIADFDDKQIEQALADVDVPIVGVGGSYHLAESYPPVHY 98
>pdb|2WFP|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase (Apo
Form) From Salmonella Typhimurium
Length = 394
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 57 CDICQEKAAFIFCVEDRALFCKDCDEPIHSPG 88
I Q AA +FCVE A+ KD + PG
Sbjct: 336 TSIGQHSAAILFCVEGEAVLRKDEQRLVLKPG 367
>pdb|3H1M|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase (Holo;
Zinc Bound)
pdb|3H1W|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase Bound
With Zinc And Yttrium
pdb|3H1Y|A Chain A, Crystal Structure Of Mannose 6-Phosphate Isomerase From
Salmonella Typhimurium Bound To Substrate (F6p)and Metal
Atom (Zn)
Length = 393
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 57 CDICQEKAAFIFCVEDRALFCKDCDEPIHSPG 88
I Q AA +FCVE A+ KD + PG
Sbjct: 335 TSIGQHSAAILFCVEGEAVLRKDEQRLVLKPG 366
>pdb|2OOL|A Chain A, Crystal Structure Of The Chromophore-Binding Domain Of An
Unusual Bacteriophytochrome Rpbphp3 From R. Palustris
pdb|2OOL|B Chain B, Crystal Structure Of The Chromophore-Binding Domain Of An
Unusual Bacteriophytochrome Rpbphp3 From R. Palustris
Length = 337
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 74 ALFCKDCD-EPIHSPGSLSANHQRFLA--TGIRVALSSSCSKDAERNISEPP 122
AL +CD EPIH PG++ + F+ T +R+A S S + E + +PP
Sbjct: 22 ALDLTECDREPIHIPGAIQPHGYLFVVSETDLRIA---SVSANVEDLLRQPP 70
>pdb|3RMY|A Chain A, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|B Chain B, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|C Chain C, Crystal Structure Of HcrD W1238A MUTANT
pdb|3RMY|D Chain D, Crystal Structure Of HcrD W1238A MUTANT
Length = 415
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 160 GKKEQLEFGELEWIADMGIFNDQLPQEALAAAEVPQLPVSQSNNLISSY--RPTKFNMPY 217
G E ++ ++ WI D IF+ +L E + Q+ N+I Y P KF+ Y
Sbjct: 183 GIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQIL----RNVIKDYWGNPLKFDTEY 238
>pdb|3OGG|A Chain A, Crystal Structure Of The Receptor Binding Domain Of
Botulinum Neurotoxin D
Length = 414
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 160 GKKEQLEFGELEWIADMGIFNDQLPQEALAAAEVPQLPVSQSNNLISSY--RPTKFNMPY 217
G E ++ ++ WI D IF+ +L E + Q+ N+I Y P KF+ Y
Sbjct: 182 GIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQIL----RNVIKDYWGNPLKFDTEY 237
>pdb|3RMX|A Chain A, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|B Chain B, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|C Chain C, Crystal Structure Of HcrD F1240A MUTANT
pdb|3RMX|D Chain D, Crystal Structure Of HcrD F1240A MUTANT
Length = 415
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 160 GKKEQLEFGELEWIADMGIFNDQLPQEALAAAEVPQLPVSQSNNLISSY--RPTKFNMPY 217
G E ++ ++ WI D IF+ +L E + Q+ N+I Y P KF+ Y
Sbjct: 183 GIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQIL----RNVIKDYWGNPLKFDTEY 238
>pdb|3N7J|A Chain A, Crystal Structure Of Botulinum Neurotoxin Serotype D
Binding Domain
Length = 415
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 160 GKKEQLEFGELEWIADMGIFNDQLPQEALAAAEVPQLPVSQSNNLISSY--RPTKFNMPY 217
G E ++ ++ WI D IF+ +L E + Q+ N+I Y P KF+ Y
Sbjct: 183 GIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQIL----RNVIKDYWGNPLKFDTEY 238
>pdb|3PME|A Chain A, Crystal Structure Of The Receptor Binding Domain Of
Botulinum Neurotoxin CD MOSAIC SEROTYPE
pdb|4F83|A Chain A, Crystal Structure Of The Receptor Binding Domain Of
Botulinum Neurotoxin Mosaic Serotype CD WITH A
TETRAETHYLENE GLYCOL MOLECULE Bound On The Hcn
Sub-Domain And A Sulfate Ion At The Putative Active Site
Length = 420
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 160 GKKEQLEFGELEWIADMGIFNDQLPQEALAAAEVPQLPVSQSNNLISSY--RPTKFNMPY 217
G E ++ ++ WI D IF+ +L E + Q+ N+I Y P KF+ Y
Sbjct: 182 GIDENIDENQMLWIRDFNIFSKELSNEDINIVYEGQIL----RNVIKDYWGNPLKFDTEY 237
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
0.317 0.131 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,898,165
Number of Sequences: 62578
Number of extensions: 258346
Number of successful extensions: 532
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 527
Number of HSP's gapped (non-prelim): 15
length of query: 238
length of database: 14,973,337
effective HSP length: 96
effective length of query: 142
effective length of database: 8,965,849
effective search space: 1273150558
effective search space used: 1273150558
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)