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= 008574
(561 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 32.3 bits (72), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 24 RLRANSKTRESPKQEAGINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPKSAEG 83
R+ +S+T SP I+ V + PE+ AR +VP + NI K R+ ++N P G
Sbjct: 317 RVDFSSRTVISPDPNISIDEVGV-PEIIARTLTVPERITPWNIEKLRQ-FVINGPDKWPG 374
Query: 84 A 84
A
Sbjct: 375 A 375
>pdb|4AT7|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex
pdb|4AT8|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex With Atp
pdb|4AT8|D Chain D, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex With Atp
pdb|4AT9|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex With Utp
pdb|4ATB|B Chain B, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex With Ctp
pdb|4ATB|D Chain D, Crystal Structure Of The Nf90-Nf45 Dimerisation Domain
Complex With Ctp
Length = 383
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 350 IQKVLAAAYTNIEDLLEFVDWLDKELSSLADERAVLKHFKWPEKKADAMREAAVEYRDLK 409
++KVLA ++ D + +D K L++LA L+H KW + +A+ ++ + R L+
Sbjct: 182 MEKVLAGETLSVNDPPDVLD-RQKCLAALAS----LRHAKWFQARANGLKSCVIVIRVLR 236
Query: 410 QLENEISSY 418
L + ++
Sbjct: 237 DLCTRVPTW 245
>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine
Synthase Rlud From Escherichia Coli
pdb|2IST|A Chain A, Crystal Structure Of Rlud From E. Coli
Length = 325
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 24 RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPK 79
R+ N K + PK++ G V+++ E++ A+ P D+ + + + +I+NKP+
Sbjct: 43 RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPR 99
>pdb|3GFF|A Chain A, Crystal Structure Of Iroe-Like Serine Hydrolase
(Np_718593.1) From Shewanella Oneidensis At 2.12 A
Resolution
pdb|3GFF|B Chain B, Crystal Structure Of Iroe-Like Serine Hydrolase
(Np_718593.1) From Shewanella Oneidensis At 2.12 A
Resolution
Length = 331
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 57/121 (47%), Gaps = 19/121 (15%)
Query: 415 ISSYRDDTNVPFGAALKKMA---------SLLDKSERSIQRLVKLRNSVMHSYKDCKIPV 465
+SSY D N+ F L K+A +++ +S+ + L + + H +KD I
Sbjct: 212 VSSYHKDLNLAFADKLTKLAPKGLGFXAKYYPEETHQSVSH-IGLYDGIRHLFKDFAI-- 268
Query: 466 DWMLDSGIISKIKQASMKLAQMYMKRVT---RELE-LVHNSDRES-TQEALLLQGL--HF 518
D DS ++ L++ + +VT + LE L+ SDR+ T+ L+GL HF
Sbjct: 269 DIYSDSFSKQQVIDQYGVLSERFGHKVTPSQQYLEQLIQYSDRQQLTERKQXLEGLRQHF 328
Query: 519 A 519
A
Sbjct: 329 A 329
>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
Pseudouridine Synthase Rlud
Length = 349
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 24 RLRANSKTRESPKQEA-GINGVSLSPELKARAKSVPADVKTNNISKSRRALILNKPK 79
R+ N K + PK++ G V+++ E++ A+ P D+ + + + +I+NKP+
Sbjct: 67 RVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPR 123
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 0.344
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,332,956
Number of Sequences: 62578
Number of extensions: 477442
Number of successful extensions: 1100
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1097
Number of HSP's gapped (non-prelim): 13
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
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: 54 (25.4 bits)