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= 025183
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex
Length = 252
Score = 176 bits (446), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 107/260 (41%), Positives = 149/260 (57%), Gaps = 33/260 (12%)
Query: 16 IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
I EV+ NL E ++IR +I +Y ++MDTEFPGVV RP R + Y L+ NVD
Sbjct: 2 ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFR-SNADYQYQLLRCNVD 60
Query: 76 LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGL--- 132
LL +IQ+GLT +E+G P G++ W+FNFK F++ +A DS+ELL G+
Sbjct: 61 LLKIIQLGLTFMNEQGEYP---PGTS--TWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK 114
Query: 133 ---------------------VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 171
VL + V W++FHS YDFGYL+K LT LPE+ +F
Sbjct: 115 KHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEI 174
Query: 172 VGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 231
+ +FF +YDVK+L++ C L GGL V + L +ER +G HQAGSDSLLT AF K++
Sbjct: 175 LRLFF-PVIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDSLLTGMAFFKMR 232
Query: 232 DKHFGNEYELQKYANVLHGL 251
+ F + + KY L+GL
Sbjct: 233 EMFFEDHIDDAKYCGHLYGL 252
>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 = 176 bits (446), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 104/260 (40%), Positives = 146/260 (56%), Gaps = 34/260 (13%)
Query: 16 IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
IR+V+ NL E I +LI+RYP++SMDTEFPGVV RP + D +Y L+ANVD
Sbjct: 23 IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSD-DYHYQTLRANVD 81
Query: 76 LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQG---- 131
L +IQIGL LSDEEGN P W+FNF F++ +A +S+ELL + G
Sbjct: 82 SLKIIQIGLALSDEEGNAPVEAC-----TWQFNFT-FNLQDDMYAPESIELLTKSGIDFK 135
Query: 132 --------------------LVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 171
LVL ++VTW+TFHS YDF YL+K +TQ LP + EF
Sbjct: 136 KHQEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKI 195
Query: 172 VGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 231
+ ++F K YD+K++++ GL + L + R +G HQAGSD+LLT F +I+
Sbjct: 196 LCIYF-PKNYDIKYIMKSVLNNSKGLQDIADDLQIHR-IGPQHQAGSDALLTARIFFEIR 253
Query: 232 DKHFGNEYELQKYANVLHGL 251
++F + + N L+GL
Sbjct: 254 SRYFDGSID-SRMLNQLYGL 272
>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 = 176 bits (446), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 107/260 (41%), Positives = 147/260 (56%), Gaps = 33/260 (12%)
Query: 16 IREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKANVD 75
I EV+ NL E ++IR +I +Y ++MDTEFPGVV RP R + Y L+ NVD
Sbjct: 12 ICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFR-SNADYQYQLLRCNVD 70
Query: 76 LLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKRQGL--- 132
LL +IQ+GLT +E+G P S W+FNFK F++ +A DS+ELL G+
Sbjct: 71 LLKIIQLGLTFMNEQGEYPPGTS-----TWQFNFK-FNLTEDMYAQDSIELLTTSGIQFK 124
Query: 133 ---------------------VLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFVTR 171
VL + V W++FHS YDFGYL+K LT LPE+ +F
Sbjct: 125 KHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEI 184
Query: 172 VGVFFGEKVYDVKHLIRFCTCLYGGLDRVCKALGVERVVGKSHQAGSDSLLTLHAFLKIK 231
+ +FF +YDVK+L++ C L GGL V + L +ER +G HQAGSDSLLT AF K++
Sbjct: 185 LRLFF-PVIYDVKYLMKSCKNLKGGLQEVAEQLELER-IGPQHQAGSDSLLTGMAFFKMR 242
Query: 232 DKHFGNEYELQKYANVLHGL 251
+ F + + KY L+GL
Sbjct: 243 EMFFEDHIDDAKYCGHLYGL 262
>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 286
Score = 118 bits (296), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 83/281 (29%), Positives = 132/281 (46%), Gaps = 50/281 (17%)
Query: 14 ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKAN 73
+ +R+V++ NL SEF IR L+ +Y +S+ TEF G + RP R + +Y ++AN
Sbjct: 11 LFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSK-VDYHYQTMRAN 69
Query: 74 VDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKR---- 129
VD LN IQ+GL+LSD GN PD G + W+FNF +FD + + +S+ELL++
Sbjct: 70 VDFLNPIQLGLSLSDANGNKPDNGPST----WQFNF-EFDPKKEIMSTESLELLRKSGIN 124
Query: 130 --------------------QGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFV 169
GL+++ VTW+T+H+AYD G+L+ L +P +F
Sbjct: 125 FEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFE 184
Query: 170 TRVGVFFGEKVYDVKHLIRFCTCLYG---------------GLDRVCKALGVERVVGKSH 214
V + YD+ + + L + LG+ R +
Sbjct: 185 WWVHQYM-PNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFT- 242
Query: 215 QAGSDSLLTLHAFL---KIKDKHFGNEYELQKYANVLHGLE 252
G SLL L +F K+ F N + KY V++G++
Sbjct: 243 TTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 283
>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 = 118 bits (296), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 83/281 (29%), Positives = 132/281 (46%), Gaps = 50/281 (17%)
Query: 14 ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKAN 73
+ +R+V++ NL SEF IR L+ +Y +S+ TEF G + RP R + +Y ++AN
Sbjct: 13 LFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSK-VDYHYQTMRAN 71
Query: 74 VDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKR---- 129
VD LN IQ+GL+LSD GN PD G + W+FNF +FD + + +S+ELL++
Sbjct: 72 VDFLNPIQLGLSLSDANGNKPDNGPST----WQFNF-EFDPKKEIMSTESLELLRKSGIN 126
Query: 130 --------------------QGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFV 169
GL+++ VTW+T+H+AYD G+L+ L +P +F
Sbjct: 127 FEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFE 186
Query: 170 TRVGVFFGEKVYDVKHLIRFCTCLYG---------------GLDRVCKALGVERVVGKSH 214
V + YD+ + + L + LG+ R +
Sbjct: 187 WWVHQYM-PNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFT- 244
Query: 215 QAGSDSLLTLHAFL---KIKDKHFGNEYELQKYANVLHGLE 252
G SLL L +F K+ F N + KY V++G++
Sbjct: 245 TTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 285
>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 = 118 bits (296), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 83/281 (29%), Positives = 132/281 (46%), Gaps = 50/281 (17%)
Query: 14 ILIREVFEFNLISEFERIRALIDRYPIISMDTEFPGVVVRPDSNIRHRDPAANYNGLKAN 73
+ +R+V++ NL SEF IR L+ +Y +S+ TEF G + RP R + +Y ++AN
Sbjct: 14 LFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSK-VDYHYQTMRAN 72
Query: 74 VDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHALDSVELLKR---- 129
VD LN IQ+GL+LSD GN PD G + W+FNF +FD + + +S+ELL++
Sbjct: 73 VDFLNPIQLGLSLSDANGNKPDNGPST----WQFNF-EFDPKKEIMSTESLELLRKSGIN 127
Query: 130 --------------------QGLVLNKDVTWVTFHSAYDFGYLVKCLTQRVLPEKLSEFV 169
GL+++ VTW+T+H+AYD G+L+ L +P +F
Sbjct: 128 FEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFE 187
Query: 170 TRVGVFFGEKVYDVKHLIRFCTCLYG---------------GLDRVCKALGVERVVGKSH 214
V + YD+ + + L + LG+ R +
Sbjct: 188 WWVHQYM-PNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFT- 245
Query: 215 QAGSDSLLTLHAFL---KIKDKHFGNEYELQKYANVLHGLE 252
G SLL L +F K+ F N + KY V++G++
Sbjct: 246 TTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGID 286
>pdb|3H49|A Chain A, Crystal Structure Of A Putative Ribokinase (Apo Form) From
E.Coli At 1.8a Resolution
pdb|3H49|B Chain B, Crystal Structure Of A Putative Ribokinase (Apo Form) From
E.Coli At 1.8a Resolution
pdb|3IN1|A Chain A, Crystal Structure Of A Putative Ribokinase In Complex With
Adp From E.Coli
pdb|3IN1|B Chain B, Crystal Structure Of A Putative Ribokinase In Complex With
Adp From E.Coli
Length = 325
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 66 NYNGLKANVDLLNLIQIGLTLSDEEGNLPDLGSGSTYYIWEFNFKDFDIARHAHA 120
+ LK +V + I +GL D E +GS +W+ N D D AR + A
Sbjct: 85 DIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGS---LWKLNIDDVDFARFSQA 136
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
0.324 0.143 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,847,916
Number of Sequences: 62578
Number of extensions: 336216
Number of successful extensions: 891
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: 863
Number of HSP's gapped (non-prelim): 7
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)