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= 038950
(297 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation
Subunit
pdb|3G0Z|A Chain A, Structure Of S. Pombe Pop2p - Zn2+ And Mn2+ Bound Form
pdb|3G10|A Chain A, Structure Of S. Pombe Pop2p - Mg2+ And Mn2+ Bound Form
Length = 333
Score = 144 bits (363), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 94/262 (35%), Positives = 140/262 (53%), Gaps = 24/262 (9%)
Query: 4 VSKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRNTPRNAPAVES-----YNDL 58
+S I +VW N + M + L+ + V+S+DTEFPG + R +S Y L
Sbjct: 20 ISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVA---RPLGVFKSSDDYHYQTL 76
Query: 59 KFNVDCTHLIQLGITLSDKEGKI---SYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFD 115
+ NVD +IQ+G+ LSD+EG + T++FNF+ F+L+ D++A +SI+LL SG+DF
Sbjct: 77 RANVDSLKIIQIGLALSDEEGNAPVEACTWQFNFT-FNLQDDMYAPESIELLTKSGIDFK 135
Query: 116 KIRKDGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGV 175
K ++ GI FA + +E + W+TFH YD AYL+K T LP E F +
Sbjct: 136 KHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKI 195
Query: 176 AALFFQSVFDIKVVAGYCXXXXXXXXXXXXXARILNVKRHGGAHHAGSDSLLTAAVFAEM 235
++F +DIK + A L + R G H AGSD+LLTA +F E+
Sbjct: 196 LCIYFPKNYDIKYI---MKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEI 252
Query: 236 KNRYELEESAFDGFLYGMDSRI 257
++RY FDG +DSR+
Sbjct: 253 RSRY------FDG---SIDSRM 265
>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
pdb|4GMJ|D Chain D, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
pdb|4GMJ|F Chain F, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 285
Score = 142 bits (358), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 87/259 (33%), Positives = 139/259 (53%), Gaps = 12/259 (4%)
Query: 5 SKILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRN--TPRNAPAVESYNDLKFNV 62
+I VW N + M+ + +++ +N +++DTEFPG + + A Y L+ NV
Sbjct: 10 QRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNV 69
Query: 63 DCTHLIQLGITLSDKEGKI---SYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRK 119
D +IQLG+T +++G+ + T++FNF F+L +D++A DSI+LL SG+ F K +
Sbjct: 70 DLLKIIQLGLTFMNEQGEYPPGTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEE 128
Query: 120 DGIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALF 179
+GI FA + E +KW++FH YD YL+KI TN LP F + LF
Sbjct: 129 EGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLF 188
Query: 180 FQSVFDIKVVAGYCXXXXXXXXXXXXXARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRY 239
F ++D+K + C A L ++R G H AGSDSLLT F +M+ +
Sbjct: 189 FPVIYDVKYLMKSC---KNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMF 245
Query: 240 ---ELEESAFDGFLYGMDS 255
++++ + G LYG+ S
Sbjct: 246 FEDHIDDAKYCGHLYGLGS 264
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex
Length = 252
Score = 141 bits (355), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 86/256 (33%), Positives = 138/256 (53%), Gaps = 12/256 (4%)
Query: 6 KILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFLRN--TPRNAPAVESYNDLKFNVD 63
+I VW N + M+ + +++ +N +++DTEFPG + + A Y L+ NVD
Sbjct: 1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD 60
Query: 64 CTHLIQLGITLSDKEGKI---SYTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKD 120
+IQLG+T +++G+ + T++FNF F+L +D++A DSI+LL SG+ F K ++
Sbjct: 61 LLKIIQLGLTFMNEQGEYPPGTSTWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKKHEEE 119
Query: 121 GIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180
GI FA + E +KW++FH YD YL+KI TN LP F + LFF
Sbjct: 120 GIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFF 179
Query: 181 QSVFDIKVVAGYCXXXXXXXXXXXXXARILNVKRHGGAHHAGSDSLLTAAVFAEMKNRY- 239
++D+K + C A L ++R G H AGSDSLLT F +M+ +
Sbjct: 180 PVIYDVKYLMKSC---KNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFF 236
Query: 240 --ELEESAFDGFLYGM 253
++++ + G LYG+
Sbjct: 237 EDHIDDAKYCGHLYGL 252
>pdb|1UOC|A Chain A, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2
Protein
pdb|1UOC|B Chain B, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2
Protein
Length = 289
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 58/189 (30%), Positives = 103/189 (54%), Gaps = 7/189 (3%)
Query: 7 ILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFL-RNTPRNAPAVE-SYNDLKFNVDC 64
+ +VW N + +L++ +N +SI TEF G L R V+ Y ++ NVD
Sbjct: 16 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 75
Query: 65 THLIQLGITLSDKEGKIS----YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKD 120
+ IQLG++LSD G T++FNF +FD KK++ + +S++LL+ SG++F+K
Sbjct: 76 LNPIQLGLSLSDANGNKPDNGPSTWQFNF-EFDPKKEIMSTESLELLRKSGINFEKHENL 134
Query: 121 GIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180
GI F+ ++ +++ W+T+H YD+ +L+ I ND++P E F +
Sbjct: 135 GIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYM 194
Query: 181 QSVFDIKVV 189
+ +D+ +V
Sbjct: 195 PNFYDLNLV 203
>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 286
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 58/189 (30%), Positives = 103/189 (54%), Gaps = 7/189 (3%)
Query: 7 ILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFL-RNTPRNAPAVE-SYNDLKFNVDC 64
+ +VW N + +L++ +N +SI TEF G L R V+ Y ++ NVD
Sbjct: 13 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 72
Query: 65 THLIQLGITLSDKEGKIS----YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKD 120
+ IQLG++LSD G T++FNF +FD KK++ + +S++LL+ SG++F+K
Sbjct: 73 LNPIQLGLSLSDANGNKPDNGPSTWQFNF-EFDPKKEIMSTESLELLRKSGINFEKHENL 131
Query: 121 GIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180
GI F+ ++ +++ W+T+H YD+ +L+ I ND++P E F +
Sbjct: 132 GIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYM 191
Query: 181 QSVFDIKVV 189
+ +D+ +V
Sbjct: 192 PNFYDLNLV 200
>pdb|4B8C|A Chain A, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|C Chain C, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|E Chain E, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|F Chain F, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 288
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 58/189 (30%), Positives = 103/189 (54%), Gaps = 7/189 (3%)
Query: 7 ILNVWCENFEIVMRFLDKLLNCFNVLSIDTEFPGFL-RNTPRNAPAVE-SYNDLKFNVDC 64
+ +VW N + +L++ +N +SI TEF G L R V+ Y ++ NVD
Sbjct: 15 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 74
Query: 65 THLIQLGITLSDKEGKIS----YTFEFNFSDFDLKKDLHAGDSIQLLKDSGLDFDKIRKD 120
+ IQLG++LSD G T++FNF +FD KK++ + +S++LL+ SG++F+K
Sbjct: 75 LNPIQLGLSLSDANGNKPDNGPSTWQFNF-EFDPKKEIMSTESLELLRKSGINFEKHENL 133
Query: 121 GIPRCVFAPRFLEVLSKHRENLKWVTFHGLYDVAYLVKIFTNDALPPTAEAFSGVAALFF 180
GI F+ ++ +++ W+T+H YD+ +L+ I ND++P E F +
Sbjct: 134 GIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYM 193
Query: 181 QSVFDIKVV 189
+ +D+ +V
Sbjct: 194 PNFYDLNLV 202
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
0.325 0.141 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,636,279
Number of Sequences: 62578
Number of extensions: 342850
Number of successful extensions: 881
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: 857
Number of HSP's gapped (non-prelim): 6
length of query: 297
length of database: 14,973,337
effective HSP length: 98
effective length of query: 199
effective length of database: 8,840,693
effective search space: 1759297907
effective search space used: 1759297907
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)