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= psy9966
(1101 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 221 bits (564), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 111/272 (40%), Positives = 168/272 (61%), Gaps = 3/272 (1%)
Query: 1 MFQVKVGNQSIVYTGDYNMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFL 60
MF +++ ++YTGD++ DRHL AA I +PD+LI ESTY T I + + RE F
Sbjct: 164 MFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFC 223
Query: 61 KKVHECVDRGGKVLIPVFALGRAQELCILLETYWERMN--LQAPIYFAVGLTEKATNYYK 118
VH+ V+RGG+ LIPVFALGRAQEL ++L+ YW+ PIY+A L +K Y+
Sbjct: 224 NTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQ 283
Query: 119 MFITWTNQKIRKTFVQRNMFDFKHIRPFDK-SFIDNPGPMVVFATPGMLHSGLSLIIFKK 177
++ N KIRK N F FKHI D+ GP VV A+PGM+ SGLS +F+
Sbjct: 284 TYVNAMNDKIRKQININNPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFES 343
Query: 178 WAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYMSFSAHADAKGIM 237
W + N +I+ G+CV+GT+ ++S +++ + Q + +KM+++Y+SFSAH D +
Sbjct: 344 WCTDKRNGVIIAGYCVEGTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTS 403
Query: 238 QLIQYCEPKNVLLVHGEASKMVFLKEKIKQEF 269
+ I+ +P +V+LVHGE ++M LK + +E+
Sbjct: 404 EFIRALKPPHVILVHGEQNEMARLKAALIREY 435
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 137 bits (345), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 89/288 (30%), Positives = 147/288 (51%), Gaps = 17/288 (5%)
Query: 7 GNQSIVYTGDYNMTPDRHLGAAWIDKCRPDLLITESTY--ATTIRDSKRCRERDFLKKVH 64
G +I TGD+ P R L A R + L+ ESTY A I+ + E+ ++ +H
Sbjct: 358 GLHNIAITGDFKFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIH 417
Query: 65 ECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFITWT 124
+ RGGKVLIP A+GRAQE+ ++LE Y ++ PIY G+ +AT + + +
Sbjct: 418 NTIKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLD-GMIWEATAIHTAYPEYL 476
Query: 125 NQKIRKTFVQR--NMFDFKHIRPFDKS-----FIDNPGPMVVFATPGMLHSGLSLIIFKK 177
++++R+ + N F + P S ID+ P ++ A+ GML G S+ FK+
Sbjct: 477 SRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQ 536
Query: 178 WAPVENNMLIMPGFCVQGTIGHKVLSGVKKL----EFENKQIIDVKMAIEYM-SFSAHAD 232
AP N +I + +GT+G +V SG++++ E ++I V M + + FS HAD
Sbjct: 537 LAPDPKNSIIFVSYQAEGTLGRQVQSGIREIPMVGEEGRTEVIKVNMEVHTIDGFSGHAD 596
Query: 233 AKGIMQLIQYCEPK--NVLLVHGEASKMVFLKEKIKQEFNLDCFMPAN 278
+ +M + P+ ++ VHGE K + L I ++F + P N
Sbjct: 597 RRELMNYVAKVRPRPERIITVHGEPQKCLDLATSIHRKFGISTRAPNN 644
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 124 bits (311), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 87/306 (28%), Positives = 155/306 (50%), Gaps = 29/306 (9%)
Query: 2 FQVKVGNQSIVYTGDYNMTPDRHLGAAWIDKCRPDLLITESTYAT--TIRDSKRCRERDF 59
+ G ++VYTGD+ R L AA R + L+ ESTY ++ S+ E++
Sbjct: 338 LHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKEL 397
Query: 60 LKKVHECVDRGGKVLIPVFALGRAQELCILLETYWERMNL-QAPIYFAVGLTEKATNYYK 118
+K ++ + RGGK+LIPVFA+GRAQEL I+LE Y + + P+Y G+ +A +
Sbjct: 398 VKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYID-GMIWEANAIHT 456
Query: 119 MFITWTNQKIRKTFVQRNMFDFKHIRPF------------DKSFIDNPGPMVVFATPGML 166
+ ++ +R +F H PF ++ I P ++ +T GML
Sbjct: 457 ARPEYLSKDLRD-----QIFHMGH-NPFISDIFHKVNGMDERREIVEGEPSIILSTSGML 510
Query: 167 HSGLSLIIFKKWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENK----QIIDVKMAI 222
G SL FK +N L+ G+ +G++G ++ G K++ +++ ++ +V+M I
Sbjct: 511 TGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNI 570
Query: 223 EYM-SFSAHADAKGIMQLIQYCEPK--NVLLVHGEASKMVFLKEKIKQEFNLDCFMPANG 279
+ + FS H+D + +M+ ++ PK +LL HG+ K + L I + + ++ P N
Sbjct: 571 KTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNL 630
Query: 280 ESCFVQ 285
E+ +Q
Sbjct: 631 ETVRIQ 636
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 116 bits (290), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 81/297 (27%), Positives = 146/297 (49%), Gaps = 18/297 (6%)
Query: 2 FQVKVGNQSIVYTGDYNMTPDRHLGAAWIDKCRPDLLITESTY--ATTIRDSKRCRERDF 59
F + G ++V+TGDY R A R + +I+E+TY A + + + E+
Sbjct: 341 FHIGDGLHNVVFTGDYKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQPALKDAEKHL 400
Query: 60 LKKVHECVDRGGKVLIPVFALGRAQELCILLETYWER-MNLQAPIYFAVGLTEKATNYYK 118
V ++RGG +IP FA+GR+QE+ I+LE + + + P+Y G+ +AT +
Sbjct: 401 QMVVKNTIERGGIAVIPAFAVGRSQEVMIVLEESIRKGLIPEVPVYLD-GMIWEATAIHA 459
Query: 119 MFITWTNQKIRKTFVQR--NMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLS 171
+ N +RK Q+ N F + +P D + I NP P V+ AT GM++ G
Sbjct: 460 THPEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVILATSGMMNGGPV 519
Query: 172 LIIFKKWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENK----QIIDVKMAIEYM-S 226
+ FK +A N L+ G+ GTIG ++ G K++ K +++ + M ++ +
Sbjct: 520 MEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGWKEIPMTGKNGSTEMLKMNMEVQVVDG 579
Query: 227 FSAHADAKGIMQLIQYCEPK--NVLLVHGEASKMVFLKEKIKQEFNLDCFMPANGES 281
FS H+D + +M+ ++ +P+ V HG+ V L + ++ ++ N E+
Sbjct: 580 FSGHSDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKIETRALTNLET 636
>pdb|3A4Y|A Chain A, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|B Chain B, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|C Chain C, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3A4Y|D Chain D, Crystal Structure Of H61a Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 100 bits (249), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 74/259 (28%), Positives = 130/259 (50%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + FS HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFSGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|3IEK|A Chain A, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|B Chain B, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|C Chain C, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEK|D Chain D, Crystal Structure Of Native Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IEL|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEL|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Ump
pdb|3IEM|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
pdb|3IEM|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8 Complexed With Rna Analog
Length = 431
Score = 100 bits (249), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 74/259 (28%), Positives = 130/259 (50%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + FS HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFSGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|3IDZ|A Chain A, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|B Chain B, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|C Chain C, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IDZ|D Chain D, Crystal Structure Of S378q Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 98.6 bits (244), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 73/259 (28%), Positives = 129/259 (49%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + F HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFQGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|3IE0|A Chain A, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|B Chain B, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|C Chain C, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE0|D Chain D, Crystal Structure Of S378y Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 98.2 bits (243), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 73/259 (28%), Positives = 129/259 (49%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + F HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFYGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|3IE2|A Chain A, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|B Chain B, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|C Chain C, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
pdb|3IE2|D Chain D, Crystal Structure Of H400v Mutant Ttha0252 From Thermus
Thermophilus Hb8
Length = 431
Score = 97.1 bits (240), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 71/256 (27%), Positives = 127/256 (49%), Gaps = 21/256 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + FS HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFSGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLV 251
++ +Q EP+ VL+V
Sbjct: 386 LLDWLQ-GEPRVVLVV 400
>pdb|3IE1|A Chain A, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|B Chain B, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|C Chain C, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
pdb|3IE1|D Chain D, Crystal Structure Of H380a Mutant Ttha0252 From Thermus
Thermophilus Hb8 Complexed With Rna
Length = 431
Score = 97.1 bits (240), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 73/259 (28%), Positives = 129/259 (49%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPMAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGPMVV A GML G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPMVVLAGSGMLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + FS A
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFSGAAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|2DKF|A Chain A, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|B Chain B, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|C Chain C, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
pdb|2DKF|D Chain D, Crystal Structure Of Ttha0252 From Thermus Thermophilus
Hb8, A Rna Degradation Protein Of The
Metallo-Beta-Lactamase Superfamily
Length = 431
Score = 94.7 bits (234), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 72/259 (27%), Positives = 127/259 (49%), Gaps = 22/259 (8%)
Query: 8 NQSIVYTGDY-----NMTPDRHLGAAWIDKCRPDLLITESTYATTIRDSKRCRERDFLKK 62
+++VY+GD ++ PD L DL++ E TY R R+FL+
Sbjct: 154 GRTLVYSGDLGNREKDVLPDPSL------PPLADLVLAEGTYGDRPHRPYRETVREFLEI 207
Query: 63 VHECVDRGGKVLIPVFALGRAQELCILLETYWERMNLQAPIYFAVGLTEKATNYYKMFIT 122
+ + + +GGKVLIP FA+ RAQE+ +L T+ R+ +APIY + + Y +
Sbjct: 208 LEKTLSQGGKVLIPTFAVERAQEILYVLYTHGHRLP-RAPIYLDSPXAGRVLSLYPRLVR 266
Query: 123 WTNQKIRKTFVQ-RNMFDFKHIRPFD-----KSFIDNPGPMVVFATPGMLHSGLSLIIFK 176
+ +++++ F+Q +N F + + K+ PGP VV A G L G L K
Sbjct: 267 YFSEEVQAHFLQGKNPFRPAGLEVVEHTEASKALNRAPGPXVVLAGSGXLAGGRILHHLK 326
Query: 177 KWAPVENNMLIMPGFCVQGTIGHKVLSGVKKLEFENKQIIDVKMAIEYM-SFSAHADAKG 235
N L+ G+ QG +G ++++ + ++ + ++ ++ + FS HA
Sbjct: 327 HGLSDPRNALVFVGYQPQGGLGAEIIARPPAVRILGEE-VPLRASVHTLGGFSGHAGQDE 385
Query: 236 IMQLIQYCEPKNVLLVHGE 254
++ +Q EP+ V+LVHGE
Sbjct: 386 LLDWLQ-GEPR-VVLVHGE 402
>pdb|2I7X|A Chain A, Structure Of Yeast Cpsf-100 (Ydh1p)
Length = 717
Score = 33.5 bits (75), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 58/143 (40%), Gaps = 15/143 (10%)
Query: 8 NQSIVYTGDYNMTPDRHLGAAWIDKC---------RPDLLITESTYATTIRDSKRCRERD 58
++ +VY +N T D L AA I RP +IT + + K+ R +
Sbjct: 171 SEKLVYAKRWNHTRDNILNAASILDATGKPLSTLMRPSAIITTLDRFGSSQPFKK-RSKI 229
Query: 59 FLKKVHECVDRGGKVLIPVFALGRAQELC-----ILLETYWERMNLQAPIYFAVGLTEKA 113
F + + + G V+IPV G+ +L +L E+ + Q P+ +
Sbjct: 230 FKDTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFESTKINAHTQVPVLILSYARGRT 289
Query: 114 TNYYKMFITWTNQKIRKTFVQRN 136
Y K + W + + KT+ RN
Sbjct: 290 LTYAKSMLEWLSPSLLKTWENRN 312
>pdb|3IO3|A Chain A, Get3 With Adp From D. Hansenii In Closed Form
Length = 348
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 37/61 (60%), Gaps = 7/61 (11%)
Query: 288 MKISIDVSVNLLKEEAVKYNSEPPNPLKERQIHGVLVIKDSSISLMDVDEACKEVGISRH 347
M+I + +++ L+++A +YN++P +PLK ++ D + S+ +DEA + + +H
Sbjct: 86 MEIDPEAAMSDLQQQASQYNNDPNDPLKS-------MMSDMTGSIPGIDEALSFMEVLKH 138
Query: 348 I 348
I
Sbjct: 139 I 139
>pdb|2YF0|A Chain A, Human Myotubularin Related Protein 6 (Mtmr6)
Length = 512
Score = 30.0 bits (66), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 456 SSSRYVQGTYYL-HTYLTSVTKHQKETMELIKNTID-EMIEFITPN----IACVNTHTVH 509
+S++ + GT YL T+L + HQKET L + E + T I C N TVH
Sbjct: 20 TSNKSLTGTLYLTATHLLFIDSHQKETWILHHHIASVEKLALTTSGCPLVIQCKNFRTVH 79
Query: 510 FMVEK 514
F+V +
Sbjct: 80 FIVPR 84
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
0.320 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,655,135
Number of Sequences: 62578
Number of extensions: 1143603
Number of successful extensions: 2882
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2847
Number of HSP's gapped (non-prelim): 19
length of query: 1101
length of database: 14,973,337
effective HSP length: 109
effective length of query: 992
effective length of database: 8,152,335
effective search space: 8087116320
effective search space used: 8087116320
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)