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= 017145
(376 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 115 bits (288), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 58/169 (34%), Positives = 95/169 (56%), Gaps = 11/169 (6%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
RD++ + L + L+K + + I+ A ++ES M + A K +Y
Sbjct: 149 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 199
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRG 326
R I N+ + NPDL+ ++ G++TPE L T +++A +++IE I ++ L+ Q
Sbjct: 200 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGA 259
Query: 327 GEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375
+ TD+F C +C ++K +YYQ+QTRSADEP+TT+ TC C RWKF
Sbjct: 260 TIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKF 308
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
Length = 179
Score = 114 bits (285), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 58/169 (34%), Positives = 95/169 (56%), Gaps = 11/169 (6%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
RD++ + L + L+K + + I+ A ++ES M + A K +Y
Sbjct: 19 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 69
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRG 326
R I N+ + NPDL+ ++ G++TPE L T +++A +++IE I ++ L+ Q
Sbjct: 70 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGA 129
Query: 327 GEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375
+ TD+F C +C ++K +YYQ+QTRSADEP+TT+ TC C RWKF
Sbjct: 130 TIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKF 178
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 112 bits (280), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 57/169 (33%), Positives = 94/169 (55%), Gaps = 11/169 (6%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
RD++ + L + L+K + + I+ A ++ES M + A K +Y
Sbjct: 13 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 63
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRG 326
R I N+ + NPDL+ ++ G++TPE L T +++A +++IE I ++ L+ Q
Sbjct: 64 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGA 123
Query: 327 GEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375
+ TD+F C +C ++K +YYQ+QTRSAD P+TT+ TC C RWKF
Sbjct: 124 TIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRWKF 172
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 108 bits (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 56/169 (33%), Positives = 93/169 (55%), Gaps = 11/169 (6%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
RD++ + L + L+K + + I+ A ++ES M + A K +Y
Sbjct: 18 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 68
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDERQRQIENIKEKALFECQRG 326
R I N+ + NPDL+ ++ G++TPE L T +++A +++IE I ++ L+ Q
Sbjct: 69 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGA 128
Query: 327 GEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKF 375
+ TD+F C +C ++K +YYQ+QTRSA P+TT+ TC C RWKF
Sbjct: 129 TIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWKF 177
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 71.2 bits (173), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 41/102 (40%), Positives = 61/102 (59%), Gaps = 4/102 (3%)
Query: 206 DSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLK 265
D R +R L + L K ++++ ++ +E A +VA +E +F + K K
Sbjct: 10 DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 65
Query: 266 YRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDE 307
YRS+MFN++D KN L K+VL GEVTP+ L+ MSPEE+AS E
Sbjct: 66 YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKE 107
>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation
Factor A Protein 2, Central Domain, Northeast Structural
Genomics Consortium (Nesg) Target Hr8682b
Length = 113
Score = 69.7 bits (169), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 39/102 (38%), Positives = 60/102 (58%), Gaps = 7/102 (6%)
Query: 206 DSSRDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGAEKLK 265
D+ R+K RE+L AL ++ D I D R++ +E +F +G + K +
Sbjct: 10 DAVRNKCREMLTAALQ---TDHDHVAI----GADCERLSAQIEECIFRDVGNTDMKYKNR 62
Query: 266 YRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDE 307
RS + N++D KNPDLR+ VL G +TP+++ M+ EEMASDE
Sbjct: 63 VRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDE 104
>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional
Machinery: Three-Dimensional Nmr Studies Of The Nucleic-
Acid Binding Domain Of Transcriptional Elongation Factor
Tfiis
Length = 50
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/44 (63%), Positives = 33/44 (75%)
Query: 333 TDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWKFC 376
TD F C +C ++ CTY Q+QTRSADEPMTT+V C C RWKFC
Sbjct: 7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC 50
>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 133
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/67 (43%), Positives = 37/67 (55%)
Query: 308 RQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCV 367
R I NI E A G + T +C +C R+ ++Q+Q RSADEPMTT+ CV
Sbjct: 65 RHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCV 124
Query: 368 NCSKRWK 374
NC RWK
Sbjct: 125 NCGHRWK 131
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 38/106 (35%), Positives = 56/106 (52%), Gaps = 15/106 (14%)
Query: 206 DSSRDKIRELLANAL----SKVTSEADEEIIDEVNACDPIRVAVSVESVMFEKLGRSTGA 261
DS R K RE+LA AL + ADEE + +E +++++ +
Sbjct: 14 DSVRLKCREMLAAALRTGDDYIAIGADEE-----------ELGSQIEEAIYQEIRNTDMK 62
Query: 262 EKLKYRSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMASDE 307
K + RS + N++D KNP+LRK VL G + P+ M+ EEMASDE
Sbjct: 63 YKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
Length = 57
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 330 TATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNCSKRWK 374
T T + C +CG +++MQTR+ DEP T + C C W+
Sbjct: 10 TLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR 54
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 11/98 (11%)
Query: 209 RDKIRELLANALSKVTSEADEEIIDEVNACDPIRVAVSVESVM--FEKLGRSTGAEKLKY 266
RD++ + L + L+K + + I+ A ++ES M + A K +Y
Sbjct: 23 RDQVLKALYDVLAKESEHPPQSIL---------HTAKAIESEMNKVNNCDTNEAAYKARY 73
Query: 267 RSIMFNIRDEKNPDLRKRVLLGEVTPERLVTMSPEEMA 304
R I N+ + NPDL+ ++ G++TPE L T +++A
Sbjct: 74 RIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>pdb|3H0G|I Chain I, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|U Chain U, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 113
Score = 35.0 bits (79), Expect = 0.076, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 337 KCSRCGQRKCTYYQMQTRSADEPMTTYVTCVNC 369
+C RC Q + +YQ +R D MT CV+C
Sbjct: 74 ECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHC 106
>pdb|1I3Q|I Chain I, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|I Chain I, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|I Chain I, Rna Polymerase Ii Elongation Complex
pdb|1K83|I Chain I, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|I Chain I, Wild Type Rna Polymerase Ii
pdb|1NT9|I Chain I, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|I Chain I, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|I Chain I, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|I Chain I, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|I Chain I, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|I Chain I, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|I Chain I, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|I Chain I, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|I Chain I, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|I Chain I, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|I Chain I, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|I Chain I, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|I Chain I, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|I Chain I, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|I Chain I, 12-Subunit Rna Polymerase Ii
pdb|2E2H|I Chain I, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|I Chain I, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|I Chain I, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|U Chain U, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|I Chain I, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|I Chain I, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|I Chain I, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|I Chain I, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|I Chain I, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|I Chain I, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|I Chain I, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|I Chain I, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|I Chain I, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|I Chain I, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|I Chain I, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|I Chain I, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|J Chain J, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|I Chain I, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|U Chain U, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|I Chain I, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|I Chain I, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|I Chain I, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|I Chain I, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|I Chain I, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|I Chain I, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|I Chain I, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|I Chain I, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|I Chain I, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3RZD|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|I Chain I, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|I Chain I, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|I Chain I, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|I Chain I, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|I Chain I, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|I Chain I, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|I Chain I, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|I Chain I, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|I Chain I, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 122
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%)
Query: 308 RQRQIENIKEKALFECQRGGEATATTDQFKCSRCGQRKCTYYQMQTRSADEPMTTYVTCV 367
R I NI E A G + T +C +C R+ ++Q Q R D M + C+
Sbjct: 45 RHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCL 104
Query: 368 NCSK 371
+CS
Sbjct: 105 SCSH 108
>pdb|3IFQ|A Chain A, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
pdb|3IFQ|B Chain B, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
Length = 553
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 14/91 (15%)
Query: 196 PKLTQLIKCNDSSRDKIRELLANALSKVTSEADE-EIIDEVNACDPIRVAVSVESVMFEK 254
P QL+ SS + I+ + A L ++ + + + ID A P+ +E +
Sbjct: 464 PLFVQLLY---SSVENIQRVAAGVLCELAQDKEAADAIDAEGASAPL-----MELLHSRN 515
Query: 255 LGRSTGAEKLKYRSIMFNIRDEKNPDLRKRV 285
G +T A +++F I ++KNPD RKRV
Sbjct: 516 EGTATYAA-----AVLFRISEDKNPDYRKRV 541
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 24/151 (15%)
Query: 189 SQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEV-NACDPIRVAVSV 247
+G + P + + C+D D++R+L K++ EE+ +E+ C + VS
Sbjct: 29 GKGCVIGPLVVAGVACSDE--DRLRKLGVKDSKKLSQGRREELAEEIRKICRTEVLKVSP 86
Query: 248 ESVMFEKLGRSTGAEKLK--YRSIMFNIRDE----KNPDLRKRVL---LGEVTPERLVTM 298
E+ + E++ T E LK Y I+ ++ E +PD+ L L E+T R+V
Sbjct: 87 EN-LDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEEITGLRVVAE 145
Query: 299 SPEE-----------MASDERQRQIENIKEK 318
+ +A ER+R+IE +KEK
Sbjct: 146 HKADEKYPLVAAASIIAKVEREREIERLKEK 176
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 40/151 (26%), Positives = 70/151 (46%), Gaps = 24/151 (15%)
Query: 189 SQGTIATPKLTQLIKCNDSSRDKIRELLANALSKVTSEADEEIIDEV-NACDPIRVAVSV 247
+G + P + + C+D D++R+L K++ EE+ +E+ C + VS
Sbjct: 21 GKGCVIGPLVVAGVACSDE--DRLRKLGVKDSKKLSQGRREELAEEIRKICRTEVLKVSP 78
Query: 248 ESVMFEKLGRSTGAEKLK--YRSIMFNIRDE----KNPDLRKRVL---LGEVTPERLVTM 298
E+ + E++ T E LK Y I+ ++ E +PD+ L L E+T R+V
Sbjct: 79 EN-LDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEEITGLRVVAE 137
Query: 299 SPEE-----------MASDERQRQIENIKEK 318
+ +A ER+R+IE +KEK
Sbjct: 138 HKADEKYPLVAAASIIAKVEREREIERLKEK 168
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
0.312 0.127 0.352
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,394,539
Number of Sequences: 62578
Number of extensions: 335568
Number of successful extensions: 669
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 651
Number of HSP's gapped (non-prelim): 24
length of query: 376
length of database: 14,973,337
effective HSP length: 100
effective length of query: 276
effective length of database: 8,715,537
effective search space: 2405488212
effective search space used: 2405488212
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)