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= 033968
(107 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|K Chain K, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|W Chain W, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 123
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 12 ATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD-PAREVLKDS 70
A +L +EDHTLAN + L D RV F GY +PHP + +RVQT D ++V+ D+
Sbjct: 30 AVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQTVEDCSPKQVIVDA 89
Query: 71 CQELMLMCRHVRSTFAK 87
+ L+ ++ F +
Sbjct: 90 AKSLITHLEEIKVNFMR 106
>pdb|1I3Q|K Chain K, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|K Chain K, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|K Chain K, Rna Polymerase Ii Elongation Complex
pdb|1K83|K Chain K, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|K Chain K, Wild Type Rna Polymerase Ii
pdb|1NT9|K Chain K, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|K Chain K, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|K Chain K, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|K Chain K, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|K Chain K, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|K Chain K, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|K Chain K, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|K Chain K, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|K Chain K, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|K Chain K, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|K Chain K, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|K Chain K, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|K Chain K, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|K Chain K, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|K Chain K, 12-Subunit Rna Polymerase Ii
pdb|2E2H|K Chain K, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|K Chain K, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|K Chain K, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|W Chain W, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|K Chain K, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|K Chain K, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|K Chain K, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|K Chain K, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|K Chain K, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|K Chain K, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|K Chain K, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|K Chain K, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|K Chain K, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|K Chain K, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|K Chain K, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|K Chain K, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|L Chain L, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|K Chain K, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|W Chain W, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|K Chain K, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|K Chain K, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|K Chain K, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|K Chain K, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|K Chain K, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|K Chain K, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|K Chain K, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|K Chain K, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|K Chain K, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|K Chain K, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|K Chain K, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|K Chain K, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|K Chain K, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|K Chain K, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|K Chain K, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|K Chain K, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|K Chain K, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|K Chain K, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|K Chain K, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 120
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 15 SLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT-GDPAREVLKDSCQE 73
+ +EDHTL N +R L D +V F Y + HP AR +R+QTT G ++ LK++C
Sbjct: 34 TFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNS 93
Query: 74 LMLMCRHVRSTF 85
++ +++ F
Sbjct: 94 IINKLGALKTNF 105
>pdb|2WAQ|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|M Chain M, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|L Chain L, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
In P21 Space Group
pdb|2Y0S|M Chain M, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
In P21 Space Group
pdb|4AYB|L Chain L, Rnap At 3.2ang
pdb|4B1O|L Chain L, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|M Chain M, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 92
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 1 MEHGAFGDQSNAT-FSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTT 59
ME +SN + EDHTL N + TL + V+F Y PHP ++ +++ T
Sbjct: 1 MEIKILKSESNYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVKILTD 60
Query: 60 GDPA-REVLKDSCQELMLMCRH 80
G A ++ L + + + +M H
Sbjct: 61 GSIAPKDALLKAIETVRVMASH 82
>pdb|2PA8|L Chain L, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE
SULFOLOBUS Solfataricus Rna Polymerase
pdb|2PMZ|L Chain L, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|X Chain X, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|L Chain L, The X-Ray Crystal Structure Of Rna Polymerase From
Archaea
pdb|3HKZ|V Chain V, The X-Ray Crystal Structure Of Rna Polymerase From
Archaea
Length = 92
Score = 38.9 bits (89), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 19 EDHTLANAVRFTLNQDPRVTFCGYSIPHPSDARVNIRVQTTGD--PAREVLK 68
EDHTL N + TL + V+F Y PHP ++ +++ T G P +LK
Sbjct: 20 EDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSITPKDALLK 71
>pdb|2WHK|A Chain A, Structure Of Bacillus Subtilis Mannanase Man26
Length = 336
Score = 30.0 bits (66), Expect = 0.37, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS 43
GAFG S+ TFS+ E D +R Q P + C Y+
Sbjct: 35 GAFGGYSHDTFSMAEADR-----IRSATGQSPAIYGCDYA 69
>pdb|2QHA|A Chain A, From Structure To Function: Insights Into The Catalytic
Substrate Specificity And Thermostability Displayed By
Bacillus Subtilis Mannanase Bcman
pdb|2QHA|B Chain B, From Structure To Function: Insights Into The Catalytic
Substrate Specificity And Thermostability Displayed By
Bacillus Subtilis Mannanase Bcman
Length = 342
Score = 30.0 bits (66), Expect = 0.37, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS 43
GAFG S+ TFS+ E D +R Q P + C Y+
Sbjct: 35 GAFGGYSHDTFSMAEADR-----IRSATGQSPAIYGCDYA 69
>pdb|3CBW|A Chain A, Crystal Structure Of The Ydht Protein From Bacillus
Subtilis
pdb|3CBW|B Chain B, Crystal Structure Of The Ydht Protein From Bacillus
Subtilis
Length = 353
Score = 30.0 bits (66), Expect = 0.37, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS 43
GAFG S+ TFS+ E D +R Q P + C Y+
Sbjct: 44 GAFGGYSHDTFSMAEADR-----IRSATGQSPAIYGCDYA 78
>pdb|3KLK|A Chain A, Crystal Structure Of Lactobacillus Reuteri N-Terminally
Truncated Glucansucrase Gtf180 In Triclinic Apo- Form
Length = 1039
Score = 27.3 bits (59), Expect = 2.2, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS----IPHPSDARVNIRVQTT 59
GA DQ +A + ++E HT A R D V + G+S P R N+R+
Sbjct: 633 GAADDQ-DARTAPSDEAHTTKTAYRSNAALDSNVIYEGFSNFIYWPTTESERTNVRIAQN 691
Query: 60 GD 61
D
Sbjct: 692 AD 693
>pdb|3KLL|A Chain A, Crystal Structure Of Lactobacillus Reuteri N-Terminally
Truncated Glucansucrase Gtf180-Maltose Complex
Length = 1039
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS----IPHPSDARVNIRVQTT 59
GA DQ +A + ++E HT A R D V + G+S P R N+R+
Sbjct: 633 GAADDQ-DARTAPSDEAHTTKTAYRSNAALDSNVIYEGFSNFIYWPTTESERTNVRIAQN 691
Query: 60 GD 61
D
Sbjct: 692 AD 693
>pdb|3HZ3|A Chain A, Lactobacillus Reuteri N-Terminally Truncated Glucansucrase
Gtf180(D1025n)-Sucrose Complex
Length = 1039
Score = 27.3 bits (59), Expect = 2.3, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 4 GAFGDQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYS----IPHPSDARVNIRVQTT 59
GA DQ +A + ++E HT A R D V + G+S P R N+R+
Sbjct: 633 GAADDQ-DARTAPSDEAHTTKTAYRSNAALDSNVIYEGFSNFIYWPTTESERTNVRIAQN 691
Query: 60 GD 61
D
Sbjct: 692 AD 693
>pdb|1XPP|A Chain A, Crystal Structure Of Ta1416,Dna-Directed Rna Polymerase
Subunit L, From Thermoplasma Acidophilum
pdb|1XPP|B Chain B, Crystal Structure Of Ta1416,Dna-Directed Rna Polymerase
Subunit L, From Thermoplasma Acidophilum
pdb|1XPP|C Chain C, Crystal Structure Of Ta1416,Dna-Directed Rna Polymerase
Subunit L, From Thermoplasma Acidophilum
pdb|1XPP|D Chain D, Crystal Structure Of Ta1416,Dna-Directed Rna Polymerase
Subunit L, From Thermoplasma Acidophilum
Length = 115
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/97 (19%), Positives = 49/97 (50%), Gaps = 4/97 (4%)
Query: 8 DQSNATFSLTEEDHTLANAVRFTLNQDPRVTFCGYSIPHP--SDARVNIRVQTTGDPARE 65
++++ T + D+TL + + +D +V Y I HP + ++ +RV+ +G P +
Sbjct: 19 EKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVK-SGKP-QS 76
Query: 66 VLKDSCQELMLMCRHVRSTFAKAVDDFRTSEKVQAMK 102
+K + ++L + + + F K + + ++A++
Sbjct: 77 AIKRAVRKLSKLYEDLGTQFQKEFQRYESDHMIKAVE 113
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
0.319 0.130 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,868,269
Number of Sequences: 62578
Number of extensions: 92267
Number of successful extensions: 162
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 157
Number of HSP's gapped (non-prelim): 11
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
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: 45 (21.9 bits)