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= 020417
(326 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZBH|A Chain A, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|B Chain B, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|C Chain C, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
pdb|1ZBH|D Chain D, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
3'- Exonuclease
Length = 299
Score = 92.0 bits (227), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 58/211 (27%), Positives = 104/211 (49%), Gaps = 32/211 (15%)
Query: 115 DFFLVLDLEGKIE----------ILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKY 164
D+ ++D E E I+EFPV++++ T+ D F ++VRP
Sbjct: 78 DYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPE---------- 127
Query: 165 IEGKYGKF-----GVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG 219
I + F G+ + D A F +V+++ + L G + + T G
Sbjct: 128 INTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLMKLKEL------GTKYKYSLLTDG 181
Query: 220 NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFG 279
+WD+ + QC++S++K PP+ +WIN++ + NFYK +S+ T + M++ + G
Sbjct: 182 SWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQ-TKLTIMLEKLGMDYDG 240
Query: 280 SHHLGIDDTKNITRVLQRMLADGARVQITAR 310
+ G+DD+KNI R+ RML DG ++I +
Sbjct: 241 RPNCGLDDSKNIARIAVRMLQDGCELRINEK 271
>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of
3'hexo, A Deddh Family Member, Bound To Ramp
Length = 204
Score = 91.7 bits (226), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 59/216 (27%), Positives = 105/216 (48%), Gaps = 28/216 (12%)
Query: 108 HKCSQDLDFFLVLDLEGKIE----------ILEFPVLMIDAKTMAFVDLFHRFVRP---S 154
H D+ ++D E E I+EFPV++++ T+ D F ++VRP +
Sbjct: 3 HXADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINT 62
Query: 155 KMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAA 214
++S+ I+ G+ + D A F +V+++ W L G + +
Sbjct: 63 QLSDFCISLT--------GITQDQVDRADTFPQVLKKVIDWXKLKEL------GTKYKYS 108
Query: 215 FATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQ 274
T G+WD + QC++S++K PP+ +WIN++ + NFYK +S+ T + ++
Sbjct: 109 LLTDGSWDXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQ-TKLTIXLEKLG 167
Query: 275 VPMFGSHHLGIDDTKNITRVLQRMLADGARVQITAR 310
G H G+DD+KNI R+ R L DG ++I +
Sbjct: 168 XDYDGRPHCGLDDSKNIARIAVRXLQDGCELRINEK 203
>pdb|4HXH|B Chain B, Structure Of Mrna Stem-loop, Human Stem-loop Binding
Protein And 3'hexo Ternary Complex
pdb|4HXH|E Chain E, Structure Of Mrna Stem-loop, Human Stem-loop Binding
Protein And 3'hexo Ternary Complex
Length = 303
Score = 91.7 bits (226), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 58/211 (27%), Positives = 100/211 (47%), Gaps = 32/211 (15%)
Query: 115 DFFLVLDLEGKIE----------ILEFPVLMIDAKTMAFVDLFHRFVRPSKMSEQHINKY 164
D+ ++D E E I+EFPV++++ T+ D F ++VRP
Sbjct: 74 DYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPE---------- 123
Query: 165 IEGKYGKF-----GVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCG 219
I + F G+ + D A F +V+++ W L G + + T G
Sbjct: 124 INTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWXKLKEL------GTKYKYSLLTDG 177
Query: 220 NWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFG 279
+WD + QC++S++K PP+ +WIN++ + NFYK +S+ T + ++ G
Sbjct: 178 SWDXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQ-TKLTIXLEKLGXDYDG 236
Query: 280 SHHLGIDDTKNITRVLQRMLADGARVQITAR 310
H G+DD+KNI R+ R L DG ++I +
Sbjct: 237 RPHCGLDDSKNIARIAVRXLQDGCELRINEK 267
>pdb|2XRI|A Chain A, Crystal Structure Of Human Eri1 Exoribonuclease 3
Length = 224
Score = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 28/226 (12%)
Query: 98 DLQVDAAAFQHKC--SQDLDFFLVLDLEGKI--------EILEFPVLMIDAKTMAFVDLF 147
DL + FQ Q +FLVLD E EI+EFP+L ++ +TM F
Sbjct: 12 DLGTENLYFQSMSFPPQRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTF 71
Query: 148 HRFVRPSKMSEQHINKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRG 207
H +V+P + + + G + + D ++V+++ + W+ + L +
Sbjct: 72 HMYVQP--VVHPQLTPFCTELTG---IIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNV- 125
Query: 208 GHLKRAAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYK---PRKSEAT 264
++ F TCG+WDLK +P QC+ + + YF +WINLK Y+F P+
Sbjct: 126 ----KSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKA-YSFAMGCWPK----N 176
Query: 265 GMMGMMKNRQVPMFGSHHLGIDDTKNITRVLQRMLADGARVQITAR 310
G++ M K + G H GIDD KNI +++ + G + T++
Sbjct: 177 GLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSK 222
>pdb|1ZBU|A Chain A, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|B Chain B, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|C Chain C, Crystal Structure Of Full-Length 3'-Exonuclease
pdb|1ZBU|D Chain D, Crystal Structure Of Full-Length 3'-Exonuclease
Length = 349
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 57/209 (27%), Positives = 103/209 (49%), Gaps = 28/209 (13%)
Query: 115 DFFLVLDLEGKIE----------ILEFPVLMIDAKTMAFVDLFHRFVRP---SKMSEQHI 161
D+ ++D E E I+EFPV++++ T+ D F ++VRP +++S+ I
Sbjct: 128 DYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCI 187
Query: 162 NKYIEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKRAAFATCGNW 221
+ G+ + D A F +V+++ L G + + T G+W
Sbjct: 188 SLT--------GITQDQVDRADTFPQVLKKVIDLXKLKEL------GTKYKYSLLTDGSW 233
Query: 222 DLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYKPRKSEATGMMGMMKNRQVPMFGSH 281
D + QC++S++K PP+ +WIN++ + NFYK +S+ T + ++ G
Sbjct: 234 DXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQ-TKLTIXLEKLGXDYDGRP 292
Query: 282 HLGIDDTKNITRVLQRMLADGARVQITAR 310
H G+DD+KNI R+ R L DG ++I +
Sbjct: 293 HCGLDDSKNIARIAVRXLQDGCELRINEK 321
>pdb|3CG7|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
pdb|3CG7|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
pdb|3CM5|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Mn
pdb|3CM5|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Mn
pdb|3CM6|A Chain A, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Er
pdb|3CM6|B Chain B, Crystal Structure Of Cell-Death Related Nuclease 4 (Crn-4)
Bound With Er
Length = 308
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 65/219 (29%), Positives = 102/219 (46%), Gaps = 32/219 (14%)
Query: 105 AFQHKCSQDLDFFLVLDLEGK---------IEILEFPVLMIDAKTMAFVD--LFHRFVRP 153
A+QH C D L+LD E E+++F ++ D + F+++V+P
Sbjct: 12 AYQH-CP--FDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKP 68
Query: 154 SKMSEQHINKYIEGKYGKF-GVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGGHLKR 212
+N+ + F G+ + DTA F V +QF+ WLI L E+G+
Sbjct: 69 V------LNRTLTKNCVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGL-EEGK------ 115
Query: 213 AAFATCGNWDLKTKVPDQCKVSQIKLPPYFMEWINLKDVFYNFYK---PRKSEATGMMGM 269
AF DL Q K+S I++P +F ++INL +F N P++ AT +G
Sbjct: 116 FAFVCDSRQDLWRIAQYQMKLSNIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGK 175
Query: 270 MKNR-QVPMFGSHHLGIDDTKNITRVLQRMLADGARVQI 307
M +P G H +DD NI +LQRM+ GA+V +
Sbjct: 176 MNEYYDLPTIGRAHDAMDDCLNIATILQRMINMGAKVTV 214
>pdb|1UGJ|A Chain A, Solution Structure Of A Murine Hypothetical Protein From
Riken Cdna 2310057j16
Length = 141
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 165 IEGKYGKFGVDRVWHDTALPFKEVIQQFEAWLIQHHLWEKGRGG 208
+EG Y K+ DR T +P K + +A+ IQ HLW+ + G
Sbjct: 96 VEGIY-KYNSDRKRF-TQIPAKTMSMSVDAFTIQGHLWQSKKSG 137
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
0.326 0.138 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,621,461
Number of Sequences: 62578
Number of extensions: 371931
Number of successful extensions: 855
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 838
Number of HSP's gapped (non-prelim): 7
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)