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= 036628
(254 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 = 101 bits (252), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 63/193 (32%), Positives = 89/193 (46%), Gaps = 40/193 (20%)
Query: 10 QDFDYFVVVDFEATCDKKIPHPQEIIEFPSVIVSGVTGQITVCFQIYA------------ 57
Q + YF+V+DFEATCDK HPQEIIEFP + ++G T +I F +Y
Sbjct: 28 QRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFC 87
Query: 58 --------------------LFLHDNWQQHMGVTPTNFA--VVTWSDWDCQVMLESECRF 95
L D W G+ N VT DWD +VML +C++
Sbjct: 88 TELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQY 147
Query: 96 KNIPKPSYFNRWINLRVPFS------KGDVRCNLKEAVELGWHGRVHCGLDDSMNIARLL 149
+P YF +WINL+ +S + ++ + + L GR H G+DD NIA ++
Sbjct: 148 LGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIM 207
Query: 150 AVIMQRGFKFSIT 162
+ RGF F T
Sbjct: 208 KTLAYRGFIFKQT 220
>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 = 77.0 bits (188), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 57/209 (27%), Positives = 92/209 (44%), Gaps = 44/209 (21%)
Query: 12 FDYFVVVDFEATCDKKIPHP--QEIIEFPSVIVSGVTGQITVCFQIYA-----LFLHDNW 64
+DY ++DFEATC++ P EIIEFP V+++ T +I FQ Y L D
Sbjct: 77 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 136
Query: 65 QQHMGVTPT----------------------------NFAVVTWSDWDCQVMLESECRFK 96
G+T ++++T WD L +C+
Sbjct: 137 ISLTGITQDQVDRADTFPQVLKKVIDLMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLS 196
Query: 97 NIPKPSYFNRWINLR--------VPFSKGDVRCNLKEAVELGWHGRVHCGLDDSMNIARL 148
+ P + +WIN+R VP S+ + L E + + + GR +CGLDDS NIAR+
Sbjct: 197 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIML-EKLGMDYDGRPNCGLDDSKNIARI 255
Query: 149 LAVIMQRGFKFSITKSLTTPQDITQDSVM 177
++Q G + I + + Q ++ S +
Sbjct: 256 AVRMLQDGCELRINEKMHAGQLMSVSSSL 284
>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 = 77.0 bits (188), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 56/195 (28%), Positives = 84/195 (43%), Gaps = 44/195 (22%)
Query: 12 FDYFVVVDFEATCDKKIPHP--QEIIEFPSVIVSGVTGQITVCFQIYA-----LFLHDNW 64
+DY ++DFEATC++ P EIIEFP V+++ T +I FQ Y L D
Sbjct: 127 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 186
Query: 65 QQHMGVTPTN----------------------------FAVVTWSDWDCQVMLESECRFK 96
G+T ++++T WD L +C+
Sbjct: 187 ISLTGITQDQVDRADTFPQVLKKVIDLXKLKELGTKYKYSLLTDGSWDXSKFLNIQCQLS 246
Query: 97 NIPKPSYFNRWINLR--------VPFSKGDVRCNLKEAVELGWHGRVHCGLDDSMNIARL 148
+ P + +WIN+R VP S+ + L E + + GR HCGLDDS NIAR+
Sbjct: 247 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXL-EKLGXDYDGRPHCGLDDSKNIARI 305
Query: 149 LAVIMQRGFKFSITK 163
+Q G + I +
Sbjct: 306 AVRXLQDGCELRINE 320
>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 = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 56/195 (28%), Positives = 86/195 (44%), Gaps = 44/195 (22%)
Query: 12 FDYFVVVDFEATCDKKIPHP--QEIIEFPSVIVSGVTGQITVCFQIYA-----LFLHD-- 62
+DY ++DFEATC++ P EIIEFP V+++ T +I FQ Y L D
Sbjct: 73 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 132
Query: 63 -------------------------NWQQHMGV-TPTNFAVVTWSDWDCQVMLESECRFK 96
+W + + T ++++T WD L +C+
Sbjct: 133 ISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLTDGSWDXSKFLNIQCQLS 192
Query: 97 NIPKPSYFNRWINLR--------VPFSKGDVRCNLKEAVELGWHGRVHCGLDDSMNIARL 148
+ P + +WIN+R VP S+ + L E + + GR HCGLDDS NIAR+
Sbjct: 193 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXL-EKLGXDYDGRPHCGLDDSKNIARI 251
Query: 149 LAVIMQRGFKFSITK 163
+Q G + I +
Sbjct: 252 AVRXLQDGCELRINE 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 = 75.5 bits (184), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 56/195 (28%), Positives = 86/195 (44%), Gaps = 44/195 (22%)
Query: 12 FDYFVVVDFEATCDKKIPHP--QEIIEFPSVIVSGVTGQITVCFQIYA-----LFLHD-- 62
+DY ++DFEATC++ P EIIEFP V+++ T +I FQ Y L D
Sbjct: 9 YDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFC 68
Query: 63 -------------------------NWQQHMGV-TPTNFAVVTWSDWDCQVMLESECRFK 96
+W + + T ++++T WD L +C+
Sbjct: 69 ISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLTDGSWDXSKFLNIQCQLS 128
Query: 97 NIPKPSYFNRWINLR--------VPFSKGDVRCNLKEAVELGWHGRVHCGLDDSMNIARL 148
+ P + +WIN+R VP S+ + L E + + GR HCGLDDS NIAR+
Sbjct: 129 RLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXL-EKLGXDYDGRPHCGLDDSKNIARI 187
Query: 149 LAVIMQRGFKFSITK 163
+Q G + I +
Sbjct: 188 AVRXLQDGCELRINE 202
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 47/202 (23%), Positives = 80/202 (39%), Gaps = 47/202 (23%)
Query: 12 FDYFVVVDFEATCDK-KIPHPQEIIEFPSVIVSGVTGQI--TVCFQIYAL---------- 58
FD +++DFE T D +P E+I+F V +I + F Y
Sbjct: 18 FDTLLILDFETTSDAANQDYPCEVIQFAIVAYDVPNDKIREDISFNKYVKPVLNRTLTKN 77
Query: 59 -------------------FLHDNWQQ---HMGVTPTNFAVVTWSDWDCQVMLESECRFK 96
+++ +QQ +G+ FA V S D + + + +
Sbjct: 78 CVDFTGIPQRSIDTADTFDVVYEQFQQWLITLGLEEGKFAFVCDSRQDLWRIAQYQMKLS 137
Query: 97 NIPKPSYFNRWINLRVPFSKGDVRCN------------LKEAVELGWHGRVHCGLDDSMN 144
NI P++F ++INL F+ R + E +L GR H +DD +N
Sbjct: 138 NIQMPAFFRQYINLYKIFTNEMDRMGPKELSATTNIGKMNEYYDLPTIGRAHDAMDDCLN 197
Query: 145 IARLLAVIMQRGFKFSITKSLT 166
IA +L ++ G K ++ + LT
Sbjct: 198 IATILQRMINMGAKVTVNELLT 219
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 0.471
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,288,645
Number of Sequences: 62578
Number of extensions: 328957
Number of successful extensions: 651
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: 628
Number of HSP's gapped (non-prelim): 13
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
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: 50 (23.9 bits)