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= 036883
(277 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 = 138 bits (347), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 78/195 (40%), Positives = 108/195 (55%), Gaps = 10/195 (5%)
Query: 1 FEYYVVIDFEATCDKERNLHPQEIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTDFCK 60
+ Y++V+DFEATCDK + +HPQEIIEFP EI + F YV+P P LT FC
Sbjct: 30 YHYFLVLDFEATCDKPQ-IHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCT 88
Query: 61 ELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFS--VVTWSDWDCQVMLESECRIK 118
ELTGI Q VD +L + L D+W+ + GL + N VT DWD +VML +C+
Sbjct: 89 ELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYL 148
Query: 119 KIQKPAYFNQWINLRVPFSKVFG----DVRCNLKEAVELAGLIWQGRVHCGLDDAINIAR 174
+ YF QWINL+ +S G + ++ + + L + GR H G+DD NIA
Sbjct: 149 GLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHI---GRPHSGIDDCKNIAN 205
Query: 175 LLSVIMRRGFKFSIT 189
++ + RGF F T
Sbjct: 206 IMKTLAYRGFIFKQT 220
>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 = 115 bits (288), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 70/197 (35%), Positives = 100/197 (50%), Gaps = 10/197 (5%)
Query: 1 FEYYVVIDFEATCDKERNLHPQ---EIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTD 57
++Y +IDFEATC E P+ EIIEFP EI FQ YVRP L+D
Sbjct: 73 YDYICIIDFEATC--EEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSD 130
Query: 58 FCKELTGIQQHQVDNGITLGEALYFHDKW--LLQMGLNNTNFSVVTWSDWDCQVMLESEC 115
FC LTGI Q QVD T + L W L ++G +S++T WD L +C
Sbjct: 131 FCISLTGITQDQVDRADTFPQVLKKVIDWXKLKELG-TKYKYSLLTDGSWDXSKFLNIQC 189
Query: 116 RIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA--GLIWQGRVHCGLDDAINIA 173
++ +++ P + +WIN+R + + R K + L G + GR HCGLDD+ NIA
Sbjct: 190 QLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSKNIA 249
Query: 174 RLLSVIMRRGFKFSITK 190
R+ ++ G + I +
Sbjct: 250 RIAVRXLQDGCELRINE 266
>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of
3'hexo, A Deddh Family Member, Bound To Ramp
Length = 204
Score = 114 bits (286), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 70/197 (35%), Positives = 100/197 (50%), Gaps = 10/197 (5%)
Query: 1 FEYYVVIDFEATCDKERNLHPQ---EIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTD 57
++Y +IDFEATC E P+ EIIEFP EI FQ YVRP L+D
Sbjct: 9 YDYICIIDFEATC--EEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSD 66
Query: 58 FCKELTGIQQHQVDNGITLGEALYFHDKW--LLQMGLNNTNFSVVTWSDWDCQVMLESEC 115
FC LTGI Q QVD T + L W L ++G +S++T WD L +C
Sbjct: 67 FCISLTGITQDQVDRADTFPQVLKKVIDWXKLKELG-TKYKYSLLTDGSWDXSKFLNIQC 125
Query: 116 RIKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA--GLIWQGRVHCGLDDAINIA 173
++ +++ P + +WIN+R + + R K + L G + GR HCGLDD+ NIA
Sbjct: 126 QLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSKNIA 185
Query: 174 RLLSVIMRRGFKFSITK 190
R+ ++ G + I +
Sbjct: 186 RIAVRXLQDGCELRINE 202
>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 = 113 bits (283), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 68/198 (34%), Positives = 101/198 (51%), Gaps = 8/198 (4%)
Query: 1 FEYYVVIDFEATCDKERNLHPQ---EIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTD 57
++Y +IDFEATC E P+ EIIEFP EI FQ YVRP L+D
Sbjct: 77 YDYICIIDFEATC--EEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSD 134
Query: 58 FCKELTGIQQHQVDNGITLGEAL-YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECR 116
FC LTGI Q QVD T + L D L+ +S++T WD L +C+
Sbjct: 135 FCISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQ 194
Query: 117 IKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAV--ELAGLIWQGRVHCGLDDAINIAR 174
+ +++ P + +WIN+R + + R K + E G+ + GR +CGLDD+ NIAR
Sbjct: 195 LSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPNCGLDDSKNIAR 254
Query: 175 LLSVIMRRGFKFSITKSL 192
+ +++ G + I + +
Sbjct: 255 IAVRMLQDGCELRINEKM 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 = 113 bits (283), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 69/196 (35%), Positives = 98/196 (50%), Gaps = 8/196 (4%)
Query: 1 FEYYVVIDFEATCDKERNLHPQ---EIIEFPXXXXXXXXXEIIACFQTYVRPTFEPLLTD 57
++Y +IDFEATC E P+ EIIEFP EI FQ YVRP L+D
Sbjct: 127 YDYICIIDFEATC--EEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSD 184
Query: 58 FCKELTGIQQHQVDNGITLGEAL-YFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECR 116
FC LTGI Q QVD T + L D L+ +S++T WD L +C+
Sbjct: 185 FCISLTGITQDQVDRADTFPQVLKKVIDLXKLKELGTKYKYSLLTDGSWDXSKFLNIQCQ 244
Query: 117 IKKIQKPAYFNQWINLRVPFSKVFGDVRCNLKEAVELA--GLIWQGRVHCGLDDAINIAR 174
+ +++ P + +WIN+R + + R K + L G + GR HCGLDD+ NIAR
Sbjct: 245 LSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYDGRPHCGLDDSKNIAR 304
Query: 175 LLSVIMRRGFKFSITK 190
+ ++ G + I +
Sbjct: 305 IAVRXLQDGCELRINE 320
>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 = 94.0 bits (232), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 61/215 (28%), Positives = 95/215 (44%), Gaps = 14/215 (6%)
Query: 1 FEYYVVIDFEATCDKERNLHPQEIIEFPXXXXXXXXXEIIA--CFQTYVRPTFEPLLTDF 58
F+ +++DFE T D +P E+I+F +I F YV+P LT
Sbjct: 18 FDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKN 77
Query: 59 CKELTGIQQHQVDNGITLGEALYFHDKWLLQMGLNNTNFSVVTWSDWDCQVMLESECRIK 118
C + TGI Q +D T +WL+ +GL F+ V S D + + + ++
Sbjct: 78 CVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLS 137
Query: 119 KIQKPAYFNQWINLRVPFSKVFG-------DVRCNLKEAVELAGLIWQGRVHCGLDDAIN 171
IQ PA+F Q+INL F+ N+ + E L GR H +DD +N
Sbjct: 138 NIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGRAHDAMDDCLN 197
Query: 172 IARLLSVIMRRGFKFSITKSLTPQANPNCLTWNRH 206
IA +L ++ G K ++ + LT C +W R
Sbjct: 198 IATILQRMINMGAKVTVNELLT-----CCASWRRQ 227
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 0.140 0.476
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,750,377
Number of Sequences: 62578
Number of extensions: 337839
Number of successful extensions: 772
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 748
Number of HSP's gapped (non-prelim): 7
length of query: 277
length of database: 14,973,337
effective HSP length: 98
effective length of query: 179
effective length of database: 8,840,693
effective search space: 1582484047
effective search space used: 1582484047
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)