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= 002393
(928 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3LWT|X Chain X, Crystal Structure Of The Yeast Sac1: Implications For Its
Phosphoinositide Phosphatase Function
Length = 505
Score = 174 bits (441), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 146/544 (26%), Positives = 236/544 (43%), Gaps = 90/544 (16%)
Query: 112 EGNRATGGLTF-----VAKVFGIAGCIKFLESYYLILVTKRRQIGCICGHAIYSIDESQL 166
+G R G F V K+ + G IK + Y I+ + G GH Y + + +
Sbjct: 37 QGVRVLGAEEFPVQGEVVKIASLMGFIKLKLNRYAIIANTVEETGRFNGHVFYRVLQHSI 96
Query: 167 ITIPHVS-IQSDVAHSKTELRYKKLLSSVDLTKDFYYSYTYPIMQSLQKN-VLSMAEEGM 224
++ S I S+ E Y KLL FY+SYTY + SLQ+N + A
Sbjct: 97 VSTKFNSRIDSE------EAEYIKLLELHLKNSTFYFSYTYDLTNSLQRNEKVGPAASWK 150
Query: 225 PYENIFVWNAYLTQPIR------LRCKNTIWTIALVHGHFKQIRLSIFGRDFSVSLISRR 278
+ F WN YLT+ +R R + I + ++G+ K + + + LI+RR
Sbjct: 151 TADERFFWNHYLTEDLRNFAHQDPRIDSFIQPV--IYGYAKTVDAVLNATPIVLGLITRR 208
Query: 279 SRHFAGTRYLKRGVNDRGRVANDVETEQVVLDEEAGSCKGKMSSVVQMRGSIPLFWSQEA 338
S AGTRY +RGV+ G V N ETEQ++L E S K + S +Q RGS+P++W+ E
Sbjct: 209 SIFRAGTRYFRRGVDKDGNVGNFNETEQILLAENPESEKIHVFSFLQTRGSVPIYWA-EI 267
Query: 339 SRFSPKPDIILQRYDPTYQATKMHFEDLAKRYGNPIIVLNLIKTVEKRPREMMLRREFAN 398
+ KP+++L + + ATK HF+ + YG+ L+ V ++ E+ ++ + +
Sbjct: 268 NNLKYKPNLVLG--ENSLDATKKHFDQQKELYGDNY----LVNLVNQKGHELPVKEGYES 321
Query: 399 AVGYLNTILSEENQVRFIHWDFHKFAKSKSANVLAVLGGVASEALDLTGFYYSGKSCITK 458
V LN + ++ ++++DFH C
Sbjct: 322 VVHALN-----DPKIHYVYFDFH-------------------------------HEC--- 342
Query: 459 KRTSQLRDLRASSGDLARVGSCNESLNSVGSRERDADFYQQSKTNSPDGAAPCFQSGVLR 518
R Q ++ L ++G NE F++ +N Q V+R
Sbjct: 343 -RKMQWHRVKLLIDHLEKLGLSNEDF-----------FHKVIDSNGNTVEIVNEQHSVVR 390
Query: 519 TNCIDCLDRTNVAQYAYGLAALGRQLHAMGLTDMPKV-NPNSSIAAALMDMYQSMGDALA 577
TNC+DCLDRTNV Q L ++ + + N+ + + +++ DA++
Sbjct: 391 TNCMDCLDRTNVVQSVLAQWVLQKEFESADVVATGSTWEDNAPLLTSYQNLWADNADAVS 450
Query: 578 QQYGGSAAHNTLRRVSYECQVFPERQGKWKATTQSREFLKSIKRYYSNAYTDGEKQDAIN 637
Y G+ A + R GK +FL S RYY N +TDG +QD+ +
Sbjct: 451 VAYSGTGA----------LKTDFTRTGKRTRLGAFNDFLNSASRYYQNNWTDGPRQDSYD 500
Query: 638 LFLG 641
LFLG
Sbjct: 501 LFLG 504
>pdb|3Q22|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gtp And
Magnesium: Substrate Complex I
pdb|3Q22|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gtp And
Magnesium: Substrate Complex I
pdb|3Q23|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gmpcpp
And Manganese: Sustrate Complex Ii
pdb|3Q23|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Gmpcpp
And Manganese: Sustrate Complex Ii
pdb|3Q0A|A Chain A, X-Ray Crystal Structure Of The Transcription Initiation
Complex Of The N4 Mini-Vrnap With P2 Promoter: Mismatch
Complex
pdb|3Q0A|B Chain B, X-Ray Crystal Structure Of The Transcription Initiation
Complex Of The N4 Mini-Vrnap With P2 Promoter: Mismatch
Complex
pdb|4FF1|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 1 Min
After Soaking Gtp, Atp And Mn
pdb|4FF1|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 1 Min
After Soaking Gtp, Atp And Mn
pdb|4FF2|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 2 Min
After Soaking Gtp, Atp And Mn
pdb|4FF2|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 2 Min
After Soaking Gtp, Atp And Mn
pdb|4FF3|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 3 Min
After Soaking Gtp, Atp And Mn
pdb|4FF3|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 3 Min
After Soaking Gtp, Atp And Mn
pdb|4FF4|A Chain A, N4 Mini-vrnap Transcription Initiation Complex, 4 Min
After Soaking Gtp, Atp And Mn
pdb|4FF4|B Chain B, N4 Mini-vrnap Transcription Initiation Complex, 4 Min
After Soaking Gtp, Atp And Mn
Length = 1118
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 769 KVTTNETANREVHRETR-----GDNFCDLNWLSSADDINDEDIFQRYSAMTYADEANGWY 823
K T N N EV + + G+ D+ A +N +D+ +R++ T EAN W
Sbjct: 86 KETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGT---EANRWV 142
Query: 824 GGTLLGDQDENSEIYKHYAELCQ 846
GG LL +++ + +K+ +L Q
Sbjct: 143 GGKLLNIVEQDGDTFKYNEQLLQ 165
>pdb|3C2P|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P1 Promoter
Complex
pdb|3C2P|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P1 Promoter
Complex
pdb|3C3L|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2 Promoter
Complex
pdb|3C3L|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2 Promoter
Complex
pdb|3C46|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2_7a
Promoter Complex Soaked With Mgcl2
pdb|3C46|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap P2_7a
Promoter Complex Soaked With Mgcl2
pdb|3Q24|A Chain A, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Pppgpg
And Pyrophosphate: Product Complex
pdb|3Q24|B Chain B, X-Ray Crystal Structure Of The N4 Mini-Vrnap And P2_7a
Promoter Transcription Initiation Complex With Pppgpg
And Pyrophosphate: Product Complex
Length = 1117
Score = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 769 KVTTNETANREVHRETR-----GDNFCDLNWLSSADDINDEDIFQRYSAMTYADEANGWY 823
K T N N EV + + G+ D+ A +N +D+ +R++ T EAN W
Sbjct: 86 KETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGT---EANRWV 142
Query: 824 GGTLLGDQDENSEIYKHYAELCQ 846
GG LL +++ + +K+ +L Q
Sbjct: 143 GGKLLNIVEQDGDTFKYNEQLLQ 165
>pdb|2PO4|A Chain A, X-Ray Crystal Structure Of Polymerase Domain Of The
Bacteriophage N4 Virion Rna Polymerase
Length = 1104
Score = 34.7 bits (78), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 769 KVTTNETANREVHRETR-----GDNFCDLNWLSSADDINDEDIFQRYSAMTYADEANGWY 823
K T N N EV + + G+ D+ A +N +D+ +R++ T EAN W
Sbjct: 74 KETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGT---EANRWV 130
Query: 824 GGTLLGDQDENSEIYKHYAELCQ 846
GG LL +++ + +K+ +L Q
Sbjct: 131 GGKLLNIVEQDGDTFKYNEQLLQ 153
>pdb|4B0E|A Chain A, Crystal Structure Of The Caf1a Usher Protein N-Terminal
Domain From Yersinia Pestis
pdb|4B0E|B Chain B, Crystal Structure Of The Caf1a Usher Protein N-Terminal
Domain From Yersinia Pestis
pdb|4B0E|C Chain C, Crystal Structure Of The Caf1a Usher Protein N-Terminal
Domain From Yersinia Pestis
pdb|4B0E|D Chain D, Crystal Structure Of The Caf1a Usher Protein N-Terminal
Domain From Yersinia Pestis
pdb|4B0M|A Chain A, Complex Of The Caf1an Usher Domain, Caf1m Chaperone And
Caf1 Subunit From Yersinia Pestis
Length = 136
Score = 30.4 bits (67), Expect = 4.7, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 622 YYSNAYTDGEKQDAINLFLGYFQPQEGKPALWELDSDYYLHVSGIGDDLFPEKCLEGSAK 681
Y+ N + +G K D+ N+ + GK LW S L GI D +P+ G+ +
Sbjct: 32 YFVNVFVNGRKVDSGNIDF-RLEKHNGKELLWPCLSSLQLTKYGIDIDKYPDLIKSGTEQ 90
Query: 682 AVGI 685
V +
Sbjct: 91 CVDL 94
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
0.319 0.134 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,346,133
Number of Sequences: 62578
Number of extensions: 1143972
Number of successful extensions: 2257
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2247
Number of HSP's gapped (non-prelim): 11
length of query: 928
length of database: 14,973,337
effective HSP length: 108
effective length of query: 820
effective length of database: 8,214,913
effective search space: 6736228660
effective search space used: 6736228660
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)