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= 023967
(274 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 298 bits (762), Expect = 2e-81, Method: Compositional matrix adjust.
Identities = 147/258 (56%), Positives = 193/258 (74%), Gaps = 7/258 (2%)
Query: 12 QIREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVD 71
+I EVW NL+EE IR+++ KYNY+AMDTEFPGVV RP+G F++ DY YQ L+ NVD
Sbjct: 11 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD 70
Query: 72 MLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKK 131
+LK+IQLGLTF +E G P GT WQFNF+ FNL +D++A DS+ELL GI FKK
Sbjct: 71 LLKIIQLGLTFMNEQGEYPP-GTS---TWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKK 125
Query: 132 NNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELI 191
+ E+GI+ F ELLM+SG+VL + V+W++FHSGYDFGYL+K+LT +LP+ + FFE++
Sbjct: 126 HEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEIL 185
Query: 192 NMYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENF 251
++FPV+YD+K+LMK C +L GGL ++AE LE+ER+G HQAGSDSLLT F K+RE F
Sbjct: 186 RLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMF 245
Query: 252 FNGCTE--KYAGVLYGLG 267
F + KY G LYGLG
Sbjct: 246 FEDHIDDAKYCGHLYGLG 263
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex
Length = 252
Score = 295 bits (754), Expect = 3e-80, Method: Compositional matrix adjust.
Identities = 146/257 (56%), Positives = 192/257 (74%), Gaps = 7/257 (2%)
Query: 12 QIREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVD 71
+I EVW NL+EE IR+++ KYNY+AMDTEFPGVV RP+G F++ DY YQ L+ NVD
Sbjct: 1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD 60
Query: 72 MLKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKK 131
+LK+IQLGLTF +E G P GT WQFNF+ FNL +D++A DS+ELL GI FKK
Sbjct: 61 LLKIIQLGLTFMNEQGEYPP-GTS---TWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKK 115
Query: 132 NNEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELI 191
+ E+GI+ F ELLM+SG+VL + V+W++FHSGYDFGYL+K+LT +LP+ + FFE++
Sbjct: 116 HEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEIL 175
Query: 192 NMYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENF 251
++FPV+YD+K+LMK C +L GGL ++AE LE+ER+G HQAGSDSLLT F K+RE F
Sbjct: 176 RLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMF 235
Query: 252 FNGCTE--KYAGVLYGL 266
F + KY G LYGL
Sbjct: 236 FEDHIDDAKYCGHLYGL 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 = 266 bits (679), Expect = 1e-71, Method: Compositional matrix adjust.
Identities = 129/256 (50%), Positives = 180/256 (70%), Gaps = 6/256 (2%)
Query: 13 IREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDM 72
IR+VW+ NL++E LI ++++Y ++MDTEFPGVV RP+G FK+ +DY+YQTL+ NVD
Sbjct: 23 IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLRANVDS 82
Query: 73 LKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKN 132
LK+IQ+GL SDE GN P + C WQFNF FNL DD++A +S+ELL + GIDFKK+
Sbjct: 83 LKIIQIGLALSDEEGNAPV----EACTWQFNFT-FNLQDDMYAPESIELLTKSGIDFKKH 137
Query: 133 NEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELIN 192
E GI+ F ELL+ SG+VL + V W+TFHSGYDF YLLK +T LP F++++
Sbjct: 138 QEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKILC 197
Query: 193 MYFPVVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFF 252
+YFP YDIK++MK + GL +A+ L++ R+G HQAGSD+LLT+ F ++R +F
Sbjct: 198 IYFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEIRSRYF 257
Query: 253 NGCTE-KYAGVLYGLG 267
+G + + LYGLG
Sbjct: 258 DGSIDSRMLNQLYGLG 273
>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 = 199 bits (505), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 107/274 (39%), Positives = 160/274 (58%), Gaps = 24/274 (8%)
Query: 13 IREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDM 72
+R+VW NL EFA+IR++V +YN++++ TEF G + RP+G F++ DY+YQT++ NVD
Sbjct: 15 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 74
Query: 73 LKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKN 132
L IQLGL+ SD NGN P G WQFNF EF+ +I +++S+ELL + GI+F+K+
Sbjct: 75 LNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLRKSGINFEKH 130
Query: 133 NEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELIN 192
GIDV F +LLM SG++++D V W+T+H+ YD G+L+ +L S+P+ + F ++
Sbjct: 131 ENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVH 190
Query: 193 MYFPVVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVGICHQAGSDS 237
Y P YD+ + K L LA+ L + R I G S
Sbjct: 191 QYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQS 250
Query: 238 ---LLTSCTFRKLRENFFNGCTE--KYAGVLYGL 266
LL+ C KL + F T+ KY GV+YG+
Sbjct: 251 LLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 284
>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 = 198 bits (504), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 107/274 (39%), Positives = 160/274 (58%), Gaps = 24/274 (8%)
Query: 13 IREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDM 72
+R+VW NL EFA+IR++V +YN++++ TEF G + RP+G F++ DY+YQT++ NVD
Sbjct: 16 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 75
Query: 73 LKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKN 132
L IQLGL+ SD NGN P G WQFNF EF+ +I +++S+ELL + GI+F+K+
Sbjct: 76 LNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLRKSGINFEKH 131
Query: 133 NEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELIN 192
GIDV F +LLM SG++++D V W+T+H+ YD G+L+ +L S+P+ + F ++
Sbjct: 132 ENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVH 191
Query: 193 MYFPVVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVGICHQAGSDS 237
Y P YD+ + K L LA+ L + R I G S
Sbjct: 192 QYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQS 251
Query: 238 ---LLTSCTFRKLRENFFNGCTE--KYAGVLYGL 266
LL+ C KL + F T+ KY GV+YG+
Sbjct: 252 LLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 285
>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 286
Score = 198 bits (504), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 107/274 (39%), Positives = 160/274 (58%), Gaps = 24/274 (8%)
Query: 13 IREVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRPVGAFKNINDYNYQTLKDNVDM 72
+R+VW NL EFA+IR++V +YN++++ TEF G + RP+G F++ DY+YQT++ NVD
Sbjct: 13 VRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDF 72
Query: 73 LKLIQLGLTFSDENGNLPTCGTDKFCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKN 132
L IQLGL+ SD NGN P G WQFNF EF+ +I +++S+ELL + GI+F+K+
Sbjct: 73 LNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLRKSGINFEKH 128
Query: 133 NEKGIDVNRFGELLMSSGIVLNDVVRWVTFHSGYDFGYLLKLLTCRSLPDTQAGFFELIN 192
GIDV F +LLM SG++++D V W+T+H+ YD G+L+ +L S+P+ + F ++
Sbjct: 129 ENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVH 188
Query: 193 MYFPVVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVGICHQAGSDS 237
Y P YD+ + K L LA+ L + R I G S
Sbjct: 189 QYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQS 248
Query: 238 ---LLTSCTFRKLRENFFNGCTE--KYAGVLYGL 266
LL+ C KL + F T+ KY GV+YG+
Sbjct: 249 LLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 282
>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain
pdb|2A1R|B Chain B, Crystal Structure Of Parn Nuclease Domain
pdb|2A1S|A Chain A, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|B Chain B, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|C Chain C, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|D Chain D, Crystal Structure Of Native Parn Nuclease Domain
Length = 430
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 36/136 (26%), Positives = 57/136 (41%), Gaps = 19/136 (13%)
Query: 15 EVWNDNLEEEFALIREIVDKYNYIAMDTEFPGVVLRP-VGAFKN---INDYNYQTLKDNV 70
E+ N + + + +++ ++ A+D EF G+ P V A N + YQ LK +
Sbjct: 2 EIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHS 61
Query: 71 DMLKLIQLGL-TFSDENGNLPTCGTDKFCIWQFNF----REFNL----IDDIFASDSVEL 121
L Q GL TF + + K+ FNF + FN + + S S++
Sbjct: 62 MDFLLFQFGLCTFKYDYTD------SKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDF 115
Query: 122 LHQCGIDFKKNNEKGI 137
L G DF K GI
Sbjct: 116 LASQGFDFNKVFRNGI 131
>pdb|2ICG|A Chain A, Crystal Structure Of A Protein Of Unknown Function
(Np_472245.1) From Listeria Innocua At 1.65 A Resolution
Length = 160
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 107 FNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGELLM 147
F++ I S+ ++ + + FK N EK + N FGE L+
Sbjct: 109 FSIDTSIIGSEGEPVIVETNLSFKDNTEKKVVANSFGEFLL 149
>pdb|1F75|A Chain A, Crystal Structure Of Undecaprenyl Diphosphate Synthase
From Micrococcus Luteus B-P 26
pdb|1F75|B Chain B, Crystal Structure Of Undecaprenyl Diphosphate Synthase
From Micrococcus Luteus B-P 26
Length = 249
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 91 TCGTDK---FCIWQFNFREFNLIDDIFASDSVELLHQCGIDFKKNNEKGIDVNRFGEL 145
T G ++ F IWQ ++ EF ID+ + + E L QC I +N + RFG L
Sbjct: 198 TSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQC-ISIYQNRHR-----RFGGL 249
>pdb|1XZP|A Chain A, Structure Of The Gtp-Binding Protein Trme From Thermotoga
Maritima
pdb|1XZQ|A Chain A, Structure Of The Gtp-binding Protein Trme From Thermotoga
Maritima Complexed With 5-formyl-thf
Length = 482
Score = 27.3 bits (59), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 202 KHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTSCTFRKLRENFFNGCTEKYAG 261
+H++K GL KL E + E I + GSDSL+T+ ++L EN +
Sbjct: 379 RHMVKISALKGEGLEKLEESIYRETQEIFER-GSDSLITNLRQKQLLENVKGHLEDAIKS 437
Query: 262 VLYGLGVE 269
+ G+ V+
Sbjct: 438 LKEGMPVD 445
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
0.323 0.142 0.437
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,934,733
Number of Sequences: 62578
Number of extensions: 390423
Number of successful extensions: 741
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 719
Number of HSP's gapped (non-prelim): 18
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)