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= 042169
(286 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VK9|A Chain A, Crystal Structure Of The Catalytic Domain Of Alpha-Toxin
From Clostridium Novyi
Length = 551
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/22 (63%), Positives = 19/22 (86%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++R+A+L KYGGVY D DF+
Sbjct: 267 SDILRIAILKKYGGVYCDLDFL 288
>pdb|4A6P|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
pdb|4A6X|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
Bound To Atp
pdb|4A6X|B Chain B, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
Bound To Atp
pdb|4A74|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
Bound To Amppnp
pdb|4A74|B Chain B, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
Bound To Amppnp
pdb|4A7O|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus
Bound To Adp
Length = 231
Score = 31.6 bits (70), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 3/108 (2%)
Query: 41 MIWFSPARTFGPRDFLAVDTLMKANPQSCL--VLISRSLDTRRGYKILKPLLDRGFKILT 98
+IW TF P + +P L + ++R+ ++ +++ D+ ++L
Sbjct: 62 VIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLN 121
Query: 99 VTPDLPSLVKDTPAEAWLKK-IKNGKIDPGKNPLSIHLSDLIRLAVLY 145
+ L+ D+ + + I G + + L+ HL+DL RLA LY
Sbjct: 122 TDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLY 169
>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 = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++RL L +GGVYLD 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 = 31.2 bits (69), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++RL L +GGVYLD D +
Sbjct: 268 SDIVRLLALKNFGGVYLDVDML 289
>pdb|3RST|A Chain A, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|B Chain B, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|C Chain C, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|D Chain D, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|E Chain E, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|F Chain F, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|G Chain G, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
pdb|3RST|H Chain H, Crystal Structure Of Bacillus Subtilis Signal Peptide
Peptidase A
Length = 240
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 53/107 (49%), Gaps = 14/107 (13%)
Query: 62 MKANPQSCLVLISRSLDTRRGYKILKPLLDRGFKILTVTPDLPSLVKDTPAEAWLKKIKN 121
+K+ + ++ SR + T+ I++ ++D ++ D+ S + P +A +KKI +
Sbjct: 138 IKSGAHADIMSPSREM-TKEEKNIMQSMVDNSYEGFV---DVISKGRGMP-KAEVKKIAD 192
Query: 122 GKIDPGKNPLSIHLSDLIRLAVLYKYGGVYLDTDFVILKDFKGLRNA 168
G++ G+ ++L D + G Y DT + KD K L+NA
Sbjct: 193 GRVYDGRQAKKLNLVDEL---------GFYDDTITAMKKDHKDLKNA 230
>pdb|1PZN|A Chain A, Rad51 (Rada)
pdb|1PZN|B Chain B, Rad51 (Rada)
pdb|1PZN|C Chain C, Rad51 (Rada)
pdb|1PZN|D Chain D, Rad51 (Rada)
pdb|1PZN|E Chain E, Rad51 (Rada)
pdb|1PZN|F Chain F, Rad51 (Rada)
pdb|1PZN|G Chain G, Rad51 (Rada)
Length = 349
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 48/108 (44%), Gaps = 3/108 (2%)
Query: 41 MIWFSPARTFGPRDFLAVDTLMKANPQSCL--VLISRSLDTRRGYKILKPLLDRGFKILT 98
+IW TF P + +P L + ++R+ ++ +++ D+ ++L
Sbjct: 168 VIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQXLLVQQAEDKIKELLN 227
Query: 99 VTPDLPSLVKDTPAEAWLKK-IKNGKIDPGKNPLSIHLSDLIRLAVLY 145
+ L+ D+ + + I G + + L+ HL+DL RLA LY
Sbjct: 228 TDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLY 275
>pdb|2VKD|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKD|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKD|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Manganese Ion
pdb|2VKH|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VKH|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VKH|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp-glc And
Calcium Ion
pdb|2VL8|A Chain A, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
pdb|2VL8|B Chain B, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
pdb|2VL8|C Chain C, Crystal Structure Of The Catalytic Domain Of Lethal Toxin
From Clostridium Sordellii In Complex With Udp,
Castanospermine And Calcium Ion
Length = 546
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 18/22 (81%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++R+++L + GGVYLD D +
Sbjct: 269 SDILRISMLKEDGGVYLDVDML 290
>pdb|1O7X|A Chain A, Citrate Synthase From Sulfolobus Solfataricus
pdb|1O7X|B Chain B, Citrate Synthase From Sulfolobus Solfataricus
pdb|1O7X|C Chain C, Citrate Synthase From Sulfolobus Solfataricus
pdb|1O7X|D Chain D, Citrate Synthase From Sulfolobus Solfataricus
Length = 377
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 50 FGPRDFLAVDTLMKANPQSCLVLISRSLDTRRGYKILKPLLDRGFK 95
FG R + D K + L LI R+ D RR ++I + L + G K
Sbjct: 256 FGHRVYKTYDPRAKIFKKLALTLIERNADARRYFEIAQKLEELGIK 301
>pdb|2BVM|A Chain A, Crystal Structure Of The Catalytic Domain Of Toxin B From
Clostridium Difficile In Complex With Udp, Glc And
Manganese Ion
Length = 542
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++R++ L + GG+YLD D +
Sbjct: 269 SDILRISALKEIGGMYLDVDML 290
>pdb|2BVL|A Chain A, Crystal Structure Of The Catalytic Domain Of Toxin B From
Clostridium Difficile In Complex With Udp, Glc And
Manganese Ion
Length = 543
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 136 SDLIRLAVLYKYGGVYLDTDFV 157
SD++R++ L + GG+YLD D +
Sbjct: 269 SDILRISALKEIGGMYLDVDML 290
>pdb|2WWB|A Chain A, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 476
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 235 YNLTILGLKAFYPVNWIQINGFYKKPVSEEESKWVEETVLELNKETYGLHLL 286
Y + +LG AF+ WI+++G K V+++ + ++ V+ ++ET +H L
Sbjct: 364 YIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKE--QQMVMRGHRETSMVHEL 413
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
0.322 0.140 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,504,084
Number of Sequences: 62578
Number of extensions: 413904
Number of successful extensions: 734
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 726
Number of HSP's gapped (non-prelim): 17
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)