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= psy3022
(258 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 197 bits (500), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 94/128 (73%), Positives = 106/128 (82%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
+ L+++FE +V+RILN ARD G SA+ SL + NN+K MV AGSKGS INISQ+ ACVGQ
Sbjct: 714 MTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQ 773
Query: 62 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 121
Q VEGKRIPFGF+ RTLPHF KDD PESRGF+ENSYL GLTP EFFFHAM GREGLIDT
Sbjct: 774 QIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDT 833
Query: 122 AVKTAETA 129
AVKTAET
Sbjct: 834 AVKTAETG 841
Score = 129 bits (323), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 62/91 (68%), Positives = 74/91 (81%)
Query: 132 AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPS 191
A +PGEMVG LAAQS+GEPATQMTLNTFH+AGVSSKNVTLGVPRLKEI+N++K K PS
Sbjct: 1059 AVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPS 1118
Query: 192 LTVFLTGQAARDAEKAKNVLCRLEHTTLRKV 222
LT++L A + + AKNV ++EHTTL V
Sbjct: 1119 LTIYLMPWIAANMDLAKNVQTQIEHTTLSTV 1149
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 195 bits (496), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 92/128 (71%), Positives = 107/128 (83%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
+ L+++FE+ V R LN+ARDK G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQ
Sbjct: 708 MTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ 767
Query: 62 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 121
Q+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDT
Sbjct: 768 QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDT 827
Query: 122 AVKTAETA 129
AVKTAET
Sbjct: 828 AVKTAETG 835
Score = 122 bits (307), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 60/87 (68%), Positives = 70/87 (80%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 195
PGEMVG LAAQS+GEPATQMTLNTFHFAGV+SK VT GVPRLKEI+N++K K PSLTV+
Sbjct: 1060 PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVY 1119
Query: 196 LTGQAARDAEKAKNVLCRLEHTTLRKV 222
L A D E+AK + +EHTTL+ V
Sbjct: 1120 LEPGHAADQEQAKLIRSAIEHTTLKSV 1146
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 194 bits (494), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 92/128 (71%), Positives = 107/128 (83%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
+ L+++FE+ V R LN+ARDK G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQ
Sbjct: 708 MTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ 767
Query: 62 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 121
Q+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDT
Sbjct: 768 QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDT 827
Query: 122 AVKTAETA 129
AVKTAET
Sbjct: 828 AVKTAETG 835
Score = 122 bits (307), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 60/87 (68%), Positives = 70/87 (80%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 195
PGEMVG LAAQS+GEPATQMTLNTFHFAGV+SK VT GVPRLKEI+N++K K PSLTV+
Sbjct: 1060 PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVY 1119
Query: 196 LTGQAARDAEKAKNVLCRLEHTTLRKV 222
L A D E+AK + +EHTTL+ V
Sbjct: 1120 LEPGHAADQEQAKLIRSAIEHTTLKSV 1146
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 194 bits (494), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 92/128 (71%), Positives = 107/128 (83%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
+ L+++FE+ V R LN+ARDK G A+ +L + NN+K MV+AGSKGS INI+Q+ ACVGQ
Sbjct: 708 MTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQ 767
Query: 62 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDT 121
Q+VEGKRI FGF RTLPHF KDDY PES+GFVENSYL GLTP EFFFHAMGGREGLIDT
Sbjct: 768 QSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDT 827
Query: 122 AVKTAETA 129
AVKTAET
Sbjct: 828 AVKTAETG 835
Score = 122 bits (307), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 60/87 (68%), Positives = 70/87 (80%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 195
PGEMVG LAAQS+GEPATQMTLNTFHFAGV+SK VT GVPRLKEI+N++K K PSLTV+
Sbjct: 1060 PGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVY 1119
Query: 196 LTGQAARDAEKAKNVLCRLEHTTLRKV 222
L A D E+AK + +EHTTL+ V
Sbjct: 1120 LEPGHAADQEQAKLIRSAIEHTTLKSV 1146
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 122 bits (305), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 58/126 (46%), Positives = 83/126 (65%)
Query: 4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
L+++ EN + L+ R G A K L +N M G++GS +NI+Q+ A +GQQ+
Sbjct: 692 LEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQS 751
Query: 64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
V G+RI G+ RTLPHF D PE+RGF+ +S+ GL P+E FFHA GGREGL+DTAV
Sbjct: 752 VRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAV 811
Query: 124 KTAETA 129
+T+++
Sbjct: 812 RTSQSG 817
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 122 bits (305), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 58/126 (46%), Positives = 83/126 (65%)
Query: 4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
L+++ EN + L+ R G A K L +N M G++GS +NI+Q+ A +GQQ+
Sbjct: 692 LEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQS 751
Query: 64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
V G+RI G+ RTLPHF D PE+RGF+ +S+ GL P+E FFHA GGREGL+DTAV
Sbjct: 752 VRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAV 811
Query: 124 KTAETA 129
+T+++
Sbjct: 812 RTSQSG 817
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 48/90 (53%), Positives = 64/90 (71%)
Query: 134 CAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLT 193
APGE +G +AAQS+GEP TQMTL TFHFAG+ NVTLG+PRL EI++ K P P +T
Sbjct: 64 IAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMT 123
Query: 194 VFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
++LT + RD +KA V +LE+T + V+
Sbjct: 124 IYLTDEYKRDRDKALEVARKLEYTKIENVV 153
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 48/90 (53%), Positives = 64/90 (71%)
Query: 134 CAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLT 193
APGE +G +AAQS+GEP TQMTL TFHFAG+ NVTLG+PRL EI++ K P P +T
Sbjct: 61 IAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMT 120
Query: 194 VFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
++LT + RD +KA V +LE+T + V+
Sbjct: 121 IYLTDEYKRDRDKALEVARKLEYTKIENVV 150
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 105 bits (263), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/90 (53%), Positives = 63/90 (70%)
Query: 134 CAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLT 193
APGE +G +AAQS+GEP TQMTL TFHFAG+ NVTLG+PRL EI++ K P P +T
Sbjct: 64 IAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMT 123
Query: 194 VFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
++LT + D EKA V +LE+T + V+
Sbjct: 124 IYLTDEYKHDKEKALEVARKLEYTKIENVV 153
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 105 bits (262), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/90 (53%), Positives = 63/90 (70%)
Query: 134 CAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLT 193
APGE +G +AAQS+GEP TQMTL TFHFAG+ NVTLG+PRL EI++ K P P +T
Sbjct: 64 IAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMT 123
Query: 194 VFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
++LT + D EKA V +LE+T + V+
Sbjct: 124 IYLTDEYKHDKEKALEVARKLEYTKIENVV 153
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 45/63 (71%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AAQS+GEP TQ+T+ TFH GV+ + ++T G+PR+ E+ +++PKA ++
Sbjct: 1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFE-ARRPKAKAVISE 1276
Query: 196 LTG 198
+ G
Sbjct: 1277 IDG 1279
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 33/141 (23%)
Query: 1 MLALKQTFE----------NQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKG 47
+L ++Q +E +Q+ ++ + +K + K+ E +N L M +G++G
Sbjct: 971 LLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARG 1030
Query: 48 SNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEF 107
+ I Q+ G ++ G V +S+ GLT E+
Sbjct: 1031 NPQQIRQLCGLRG--------------------LMQKPSGETFEVPVRSSFREGLTVLEY 1070
Query: 108 FFHAMGGREGLIDTAVKTAET 128
F + G R+G DTA++TA++
Sbjct: 1071 FISSHGARKGGADTALRTADS 1091
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 45/63 (71%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AAQS+GEP TQ+T+ TFH GV+ + ++T G+PR+ E+ +++PKA ++
Sbjct: 1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFE-ARRPKAKAVISE 1276
Query: 196 LTG 198
+ G
Sbjct: 1277 IDG 1279
Score = 35.0 bits (79), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 31/141 (21%), Positives = 60/141 (42%), Gaps = 33/141 (23%)
Query: 1 MLALKQTFE----------NQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKG 47
+L ++Q +E +Q+ ++ + +K + K+ E +N L M +G++G
Sbjct: 971 LLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARG 1030
Query: 48 SNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEF 107
+ I Q+ G ++ G V +S+ GLT E+
Sbjct: 1031 NPQQIRQLCGLRG--------------------LMQKPSGETFEVPVRSSFREGLTVLEY 1070
Query: 108 FFHAMGGREGLIDTAVKTAET 128
F + G R+G DTA++TA++
Sbjct: 1071 FISSHGARKGGADTALRTADS 1091
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AA+S+GEP TQ+T+ TFH GV+ ++T G+PR+ E+ +++PKA ++
Sbjct: 1218 GEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFE-ARRPKAKAVISE 1276
Query: 196 LTG 198
+ G
Sbjct: 1277 IDG 1279
Score = 35.0 bits (79), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 53/122 (43%), Gaps = 23/122 (18%)
Query: 10 NQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEG 66
+QV ++ + +K + K+ E +N L M +G++G+ I Q+ G
Sbjct: 990 DQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG------ 1043
Query: 67 KRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTA 126
++ G V +S+ GLT E+F + G R+G DTA++TA
Sbjct: 1044 --------------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA 1089
Query: 127 ET 128
++
Sbjct: 1090 DS 1091
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AA+S+GEP TQ+T+ TFH GV+ ++T G+PR+ E+ +++PKA ++
Sbjct: 927 GEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFE-ARRPKAKAVISE 985
Query: 196 LTG 198
+ G
Sbjct: 986 IDG 988
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 53/122 (43%), Gaps = 23/122 (18%)
Query: 10 NQVNRILNDARDKTGGSAKKSLTE---YNNLKAMVVAGSKGSNINISQVIACVGQQNVEG 66
+QV ++ + +K + K+ E +N L M +G++G+ I Q+ G
Sbjct: 699 DQVIQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG------ 752
Query: 67 KRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTA 126
++ G V +S+ GLT E+F + G R+G DTA++TA
Sbjct: 753 --------------LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA 798
Query: 127 ET 128
++
Sbjct: 799 DS 800
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AA+S+GEP TQ+T+ TFH GV+ ++T G+PR+ E+ +++PKA ++
Sbjct: 958 GEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFE-ARRPKAKAVISE 1016
Query: 196 LTG 198
+ G
Sbjct: 1017 IDG 1019
Score = 33.9 bits (76), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 94 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 797 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 831
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
Includes Complete Structure With Side-Chains (Except For
Disordered Regions)-Further Refined From Original
Deposition-Contains Additional Sequence Information
Length = 1265
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVS-SKNVTLGVPRLKEIINISKKPKAPSLTVF 195
GE VG +AA+S+GEP TQ+T+ TFH GV+ ++T G+PR+ E+ +++PKA ++
Sbjct: 959 GEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFE-ARRPKAKAVISE 1017
Query: 196 LTG 198
+ G
Sbjct: 1018 IDG 1020
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 94 VENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
V +S+ GLT E+F + G R+G DTA++TA++
Sbjct: 798 VRSSFREGLTVLEYFISSHGARKGGADTALRTADS 832
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 22/28 (78%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAG 164
GE +G +AAQS+GEP TQ+T+ TFH G
Sbjct: 912 GEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 21/104 (20%)
Query: 25 GSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKD 84
G +K ++ +N++ M +G++GS I Q+ G + + K P G T
Sbjct: 711 GQEEKQVS-FNSIYMMADSGARGSAAQIRQL---AGMRGLMAK--PDGSIIET------- 757
Query: 85 DYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
P + F E GL ++F G R+GL DTA+KTA +
Sbjct: 758 ---PITANFRE-----GLNVLQYFISTHGARKGLADTALKTANS 793
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 22/28 (78%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAG 164
GE +G +AAQS+GEP TQ+T+ TFH G
Sbjct: 912 GEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 21/104 (20%)
Query: 25 GSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKD 84
G +K ++ +N++ M +G++GS I Q+ G + + K P G T
Sbjct: 711 GQEEKQVS-FNSIYMMADSGARGSAAQIRQL---AGMRGLMAK--PDGSIIET------- 757
Query: 85 DYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
P + F E GL ++F G R+GL DTA+KTA +
Sbjct: 758 ---PITANFRE-----GLNVLQYFISTHGARKGLADTALKTANS 793
>pdb|2R6G|A Chain A, The Crystal Structure Of The E. Coli Maltose Transporter
pdb|2R6G|B Chain B, The Crystal Structure Of The E. Coli Maltose Transporter
Length = 381
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 193 TVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIILRPATHYQVELISGARRVASL 247
+VFL Q + + A V R+E + L K L + TH QVE ++ A ++ L
Sbjct: 153 SVFLLDQPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQVEAMTLADKIVVL 207
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 0.134 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,184,867
Number of Sequences: 62578
Number of extensions: 281374
Number of successful extensions: 620
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 590
Number of HSP's gapped (non-prelim): 32
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)