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= 024845
(261 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CN2|A Chain A, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|B Chain B, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|C Chain C, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|D Chain D, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
Length = 737
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 130 RHFLYYNTLRLFASEESLLSRADTKVKQLRQSIDRLKAESEKLEKVALVA-EDELIR 185
+ + +YN + + S + L+ DTK QL +S++++KA K V L A E L R
Sbjct: 579 KFYAFYNG-KFYISTDGGLTFTDTKAPQLPKSVNKIKAVPGKEGHVWLAAREGGLWR 634
>pdb|2CN3|A Chain A, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN3|B Chain B, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
Length = 737
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 130 RHFLYYNTLRLFASEESLLSRADTKVKQLRQSIDRLKAESEKLEKVALVA-EDELIR 185
+ + +YN + + S + L+ DTK QL +S++++KA K V L A E L R
Sbjct: 579 KFYAFYNG-KFYISTDGGLTFTDTKAPQLPKSVNKIKAVPGKEGHVWLAAREGGLWR 634
>pdb|3HCY|A Chain A, The Crystal Structure Of The Domain Of Putative
Two-component Sensor Histidine Kinase Protein From
Sinorhizobium Meliloti 1021
pdb|3HCY|B Chain B, The Crystal Structure Of The Domain Of Putative
Two-component Sensor Histidine Kinase Protein From
Sinorhizobium Meliloti 1021
Length = 151
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 30/69 (43%), Gaps = 11/69 (15%)
Query: 100 VKEGIHVAASHPFITAGGAIGLGSFLLKRPRHFLYYNTLRLFASEESLLSRADTKVKQLR 159
V EGI P +T G IG + YY+ FA E + A T +QL
Sbjct: 86 VGEGIAALGFFPLVTEGRLIG---------KFMTYYDRPHRFADSE--IGMALTIARQLG 134
Query: 160 QSIDRLKAE 168
SI R++AE
Sbjct: 135 FSIQRMRAE 143
>pdb|3IKO|B Chain B, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|E Chain E, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|H Chain H, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
Length = 442
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 56 AIEASRSRLSQTRLTASVHFQQTLDYLQDVKSEYAAYEDAAVGKVKEGIHVAASHPFITA 115
IEA +S +S+ F+ LDY++ S+Y ++ +++ + S+P+ T
Sbjct: 88 TIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSI------LFDPVSYPYKTD 141
Query: 116 GGAIGLGSFLLKRPRH 131
+ + LLK+ RH
Sbjct: 142 NDQVKMA--LLKKERH 155
>pdb|3BG0|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|B Chain B, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|C Chain C, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|F Chain F, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|G Chain G, Architecture Of A Coat For The Nuclear Pore Membrane
Length = 442
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 56 AIEASRSRLSQTRLTASVHFQQTLDYLQDVKSEYAAYEDAAVGKVKEGIHVAASHPFITA 115
IEA +S +S+ F+ LDY++ S+Y ++ +++ + S+P+ T
Sbjct: 88 TIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSI------LFDPVSYPYKTD 141
Query: 116 GGAIGLGSFLLKRPRH 131
+ + LLK+ RH
Sbjct: 142 NDQVKMA--LLKKERH 155
>pdb|2XCS|B Chain B, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCS|D Chain D, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCT|B Chain B, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|D Chain D, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|S Chain S, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|U Chain U, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
Length = 692
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 69/168 (41%), Gaps = 24/168 (14%)
Query: 59 ASRSRLSQTRLTASVHFQQTLDYLQDVKSEYAAYEDAAVGKVKEGIHVAASHPFITAGGA 118
A+ R ++ R+T + TL+ L+D+ + + D G +E + A P + A GA
Sbjct: 319 AAAMRFTEARMT-----KITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGA 373
Query: 119 IGLGSFLLKR-PRHFLYYNTLRLFASEESLLSRADTKVKQLRQSIDRLKAESEKLEKVAL 177
G+ + P H N L SL D + +L + I E
Sbjct: 374 SGIAVGMATNIPPH----NLTELINGVLSLSKNPDISIAELMEDI-----EGPDFPTAG- 423
Query: 178 VAEDELIRGRTKLRQAGKQIQGVIN--SAYKIERQAAGLKDI-VGELP 222
LI G++ +R+A + +G I S IE + G + I V E+P
Sbjct: 424 -----LILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIP 466
>pdb|2XCR|B Chain B, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|D Chain D, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|S Chain S, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|U Chain U, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
Length = 726
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 69/168 (41%), Gaps = 24/168 (14%)
Query: 59 ASRSRLSQTRLTASVHFQQTLDYLQDVKSEYAAYEDAAVGKVKEGIHVAASHPFITAGGA 118
A+ R ++ R+T + TL+ L+D+ + + D G +E + A P + A GA
Sbjct: 353 AAAMRFTEARMT-----KITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGA 407
Query: 119 IGLGSFLLKR-PRHFLYYNTLRLFASEESLLSRADTKVKQLRQSIDRLKAESEKLEKVAL 177
G+ + P H N L SL D + +L + I E
Sbjct: 408 SGIAVGMATNIPPH----NLTELINGVLSLSKNPDISIAELMEDI-----EGPDFPTAG- 457
Query: 178 VAEDELIRGRTKLRQAGKQIQGVIN--SAYKIERQAAGLKDI-VGELP 222
LI G++ +R+A + +G I S IE + G + I V E+P
Sbjct: 458 -----LILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIP 500
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
0.313 0.127 0.334
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,191,636
Number of Sequences: 62578
Number of extensions: 213691
Number of successful extensions: 545
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 525
Number of HSP's gapped (non-prelim): 37
length of query: 261
length of database: 14,973,337
effective HSP length: 97
effective length of query: 164
effective length of database: 8,903,271
effective search space: 1460136444
effective search space used: 1460136444
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)