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= 003896
(788 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EF1|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 442
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 58/117 (49%), Gaps = 16/117 (13%)
Query: 246 PENRDTSVLVRLRPAWEDLRSYLIAKGRKRFEVYVCTMAERDYALEMWRLLDPEGHLIGS 305
P + ++ RP + + K + +E+++ TM + YA E+ +++DP G L
Sbjct: 73 PSGYTSCYYIKFRPGL----AQFLQKISELYELHIYTMGTKAYAKEVAKIIDPTGKLFQ- 127
Query: 306 KQLLDRVVCVK-SGS--RKSLLNVFQRGLCHPKMAMVIDDRCKVWEDKDQPRVHVVP 359
DRV+ SGS +KSL +F C M +VIDDR VW D + + VVP
Sbjct: 128 ----DRVLSRDDSGSLAQKSLRRLFP---CDTSMVVVIDDRGDVW-DWNPNLIKVVP 176
>pdb|3EF0|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 372
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 58/117 (49%), Gaps = 16/117 (13%)
Query: 246 PENRDTSVLVRLRPAWEDLRSYLIAKGRKRFEVYVCTMAERDYALEMWRLLDPEGHLIGS 305
P + ++ RP + + K + +E+++ TM + YA E+ +++DP G L
Sbjct: 65 PSGYTSCYYIKFRPG----LAQFLQKISELYELHIYTMGTKAYAKEVAKIIDPTGKLFQ- 119
Query: 306 KQLLDRVVCVK-SGS--RKSLLNVFQRGLCHPKMAMVIDDRCKVWEDKDQPRVHVVP 359
DRV+ SGS +KSL +F C M +VIDDR VW D + + VVP
Sbjct: 120 ----DRVLSRDDSGSLAQKSLRRLFP---CDTSMVVVIDDRGDVW-DWNPNLIKVVP 168
>pdb|1RC7|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Ds-Rna At 2.15 Angstrom
Resolution
Length = 220
Score = 32.7 bits (73), Expect = 0.87, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 630 VLQEIG-KRCSSKVEFR--SVVSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENA 686
+LQEI KR + E+R SV +F VE E +G GK++K+A+Q+AAE
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIK-EYRTLGEGKSKKEAEQRAAEEL 213
Query: 687 LHYLAE 692
+ L E
Sbjct: 214 IKLLEE 219
>pdb|1YYO|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
pdb|1YYO|B Chain B, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
Length = 221
Score = 32.3 bits (72), Expect = 0.91, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 630 VLQEIG-KRCSSKVEFR--SVVSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENA 686
+LQEI KR + E+R SV +F VE E +G GK++K+A+Q+AAE
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIK-EYRTLGEGKSKKEAEQRAAEEL 213
Query: 687 LHYLAE 692
+ L E
Sbjct: 214 IKLLEE 219
>pdb|1YZ9|A Chain A, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
pdb|1YZ9|B Chain B, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
Length = 221
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 630 VLQEIG-KRCSSKVEFR--SVVSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENA 686
+LQEI KR + E+R SV +F VE E +G GK++K+A+Q+AAE
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIK-EYRTLGEGKSKKEAEQRAAEEL 213
Query: 687 LHYLAE 692
+ L E
Sbjct: 214 IKLLEE 219
>pdb|1YYK|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYK|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYW|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|C Chain C, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|D Chain D, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|2NUE|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUE|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUF|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUF|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUG|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
pdb|2NUG|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
Length = 221
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 630 VLQEIG-KRCSSKVEFR--SVVSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENA 686
+LQEI KR + E+R SV +F VE E +G GK++K+A+Q+AAE
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIK-EYRTLGEGKSKKEAEQRAAEEL 213
Query: 687 LHYLAE 692
+ L E
Sbjct: 214 IKLLEE 219
>pdb|2EZ6|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
pdb|2EZ6|B Chain B, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
Length = 221
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 630 VLQEIG-KRCSSKVEFR--SVVSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENA 686
+LQEI KR + E+R SV +F VE E +G GK++K+A+Q+AAE
Sbjct: 155 ILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIK-EYRTLGEGKSKKEAEQRAAEEL 213
Query: 687 LHYLAE 692
+ L E
Sbjct: 214 IKLLEE 219
>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
Length = 252
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 653 DLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENALHYLAEK 693
D F VEV G+ I G G+T+K+A+++AA A L ++
Sbjct: 210 DRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKLLKE 250
>pdb|2KHX|A Chain A, Drosha Double-Stranded Rna Binding Motif
Length = 85
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 648 VSTSKDLQFSVEVLFTGEKIGVGMGKTRKDAQQQAAENALHYLAEKY 694
V S ++V V F GE+IG G G + + A+ AA +AL EKY
Sbjct: 32 VGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDAL----EKY 74
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
0.316 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,976,512
Number of Sequences: 62578
Number of extensions: 942689
Number of successful extensions: 1881
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1879
Number of HSP's gapped (non-prelim): 9
length of query: 788
length of database: 14,973,337
effective HSP length: 107
effective length of query: 681
effective length of database: 8,277,491
effective search space: 5636971371
effective search space used: 5636971371
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)