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= 016965
(379 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XRI|A Chain A, Crystal Structure Of Human Eri1 Exoribonuclease 3
Length = 224
Score = 145 bits (365), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 78/198 (39%), Positives = 116/198 (58%), Gaps = 4/198 (2%)
Query: 130 FQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLL 189
F PQ + YF+V+DFEATCDK + +PQEIIEFP + ++ T ++E+ F YV+P + L
Sbjct: 25 FPPQRYHYFLVLDFEATCDKPQI-HPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQL 83
Query: 190 SDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNF--AVVTWSNWDCRVMLES 247
+ FC +LTGI Q VD +L + L R D+W+ +G+ + N VT +WD +VML
Sbjct: 84 TPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPG 143
Query: 248 ECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQGRAHCGLDDAKNT 306
+C++ + YF +WINLK + G + L + + L GR H G+DD KN
Sbjct: 144 QCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNI 203
Query: 307 ARLLALLMHRGFKFSITN 324
A ++ L +RGF F T+
Sbjct: 204 ANIMKTLAYRGFIFKQTS 221
>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 = 136 bits (343), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 72/198 (36%), Positives = 109/198 (55%), Gaps = 4/198 (2%)
Query: 129 DFQPQEFQYFVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQ 187
+F + Y +IDFEATC++ P + EIIEFP V++++ T ++E FQ YVRP N
Sbjct: 67 NFADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINT 126
Query: 188 LLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNT-NFAVVTWSNWDCRVMLE 246
LSDFC LTGI Q QVDR T + L + W + K + ++++T +WD L
Sbjct: 127 QLSDFCISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLTDGSWDXSKFLN 186
Query: 247 SECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAV--EMAGLAWQGRAHCGLDDAK 304
+C+ ++ PP+ +WIN++ + + R K + E G + GR HCGLDD+K
Sbjct: 187 IQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSK 246
Query: 305 NTARLLALLMHRGFKFSI 322
N AR+ + G + I
Sbjct: 247 NIARIAVRXLQDGCELRI 264
>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of
3'hexo, A Deddh Family Member, Bound To Ramp
Length = 204
Score = 135 bits (340), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 71/192 (36%), Positives = 107/192 (55%), Gaps = 4/192 (2%)
Query: 135 FQYFVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFC 193
+ Y +IDFEATC++ P + EIIEFP V++++ T ++E FQ YVRP N LSDFC
Sbjct: 9 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 68
Query: 194 KDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNT-NFAVVTWSNWDCRVMLESECRFK 252
LTGI Q QVDR T + L + W + K + ++++T +WD L +C+
Sbjct: 69 ISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLTDGSWDXSKFLNIQCQLS 128
Query: 253 KIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAV--EMAGLAWQGRAHCGLDDAKNTARLL 310
++ PP+ +WIN++ + + R K + E G + GR HCGLDD+KN AR+
Sbjct: 129 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSKNIARIA 188
Query: 311 ALLMHRGFKFSI 322
+ G + I
Sbjct: 189 VRXLQDGCELRI 200
>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 = 135 bits (339), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 70/202 (34%), Positives = 112/202 (55%), Gaps = 4/202 (1%)
Query: 129 DFQPQEFQYFVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQ 187
+F + Y +IDFEATC++ P + EIIEFP V++++ T ++E FQ YVRP N
Sbjct: 71 NFADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINT 130
Query: 188 LLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNT-NFAVVTWSNWDCRVMLE 246
LSDFC LTGI Q QVDR T + L + ++ K + ++++T +WD L
Sbjct: 131 QLSDFCISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLN 190
Query: 247 SECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAV--EMAGLAWQGRAHCGLDDAK 304
+C+ ++ PP+ +WIN++ + + R K + E G+ + GR +CGLDD+K
Sbjct: 191 IQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPNCGLDDSK 250
Query: 305 NTARLLALLMHRGFKFSITNSL 326
N AR+ ++ G + I +
Sbjct: 251 NIARIAVRMLQDGCELRINEKM 272
>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 = 132 bits (333), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 71/198 (35%), Positives = 108/198 (54%), Gaps = 4/198 (2%)
Query: 129 DFQPQEFQYFVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQ 187
+F + Y +IDFEATC++ P + EIIEFP V++++ T ++E FQ YVRP N
Sbjct: 121 NFADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINT 180
Query: 188 LLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNT-NFAVVTWSNWDCRVMLE 246
LSDFC LTGI Q QVDR T + L + + K + ++++T +WD L
Sbjct: 181 QLSDFCISLTGITQDQVDRADTFPQVLKKVIDLXKLKELGTKYKYSLLTDGSWDXSKFLN 240
Query: 247 SECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAV--EMAGLAWQGRAHCGLDDAK 304
+C+ ++ PP+ +WIN++ + + R K + E G + GR HCGLDD+K
Sbjct: 241 IQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSK 300
Query: 305 NTARLLALLMHRGFKFSI 322
N AR+ + G + I
Sbjct: 301 NIARIAVRXLQDGCELRI 318
>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 = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/206 (27%), Positives = 90/206 (43%), Gaps = 9/206 (4%)
Query: 130 FQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQ 187
+Q F +++DFE T D YP E+I+F V ++ + F YV+P N+
Sbjct: 13 YQHCPFDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNR 72
Query: 188 LLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLES 247
L+ C D TGI Q +D T + +WL G++ FA V S D + +
Sbjct: 73 TLTKNCVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQY 132
Query: 248 ECRFKKIWKPPYFNRWINLKVPFHEVFG-------GVRCNLKEAVEMAGLAWQGRAHCGL 300
+ + I P +F ++INL F N+ + E L GRAH +
Sbjct: 133 QMKLSNIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGRAHDAM 192
Query: 301 DDAKNTARLLALLMHRGFKFSITNSL 326
DD N A +L +++ G K ++ L
Sbjct: 193 DDCLNIATILQRMINMGAKVTVNELL 218
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
0.322 0.136 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,849,909
Number of Sequences: 62578
Number of extensions: 550590
Number of successful extensions: 1002
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 979
Number of HSP's gapped (non-prelim): 6
length of query: 379
length of database: 14,973,337
effective HSP length: 100
effective length of query: 279
effective length of database: 8,715,537
effective search space: 2431634823
effective search space used: 2431634823
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)