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= psy15973
(266 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P8J|A Chain A, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|B Chain B, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|C Chain C, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|D Chain D, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|E Chain E, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|F Chain F, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|G Chain G, Crystal Structure Of The Proprotein Convertase Furin
pdb|1P8J|H Chain H, Crystal Structure Of The Proprotein Convertase Furin
Length = 471
Score = 295 bits (755), Expect = 2e-80, Method: Compositional matrix adjust.
Identities = 149/212 (70%), Positives = 167/212 (78%), Gaps = 3/212 (1%)
Query: 58 GVRMLDGDVTDAVEARSLSLNPGHIDIYSASWGPDDDGKTVDGPGELATRAFIEGVTRGR 117
GVRMLDG+VTDAVEARSL LNP HI IYSASWGP+DDGKTVDGP LA AF GV++GR
Sbjct: 116 GVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGR 175
Query: 118 EGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLSTSSATETGQVPWYSEACSSTLATTYS 177
G GSIFVWASGNGGR+HD+CNCDGYTNSI+TLS SSAT+ G VPWYSEACSSTLATTYS
Sbjct: 176 GGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYS 235
Query: 178 SGSSFEHQVVTTDLHHDCTSNHTGL---APLAAGICAWPSRPNPASRGVTCRHIVVAPAR 234
SG+ E Q+VTTDL CT +HTG APLAAGI A N +H+VV ++
Sbjct: 236 SGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSK 295
Query: 235 PANLRAPDWATNGVGRNVSHSFGYGLMDATAM 266
PA+L A DWATNGVGR VSHS+GYGL+DA AM
Sbjct: 296 PAHLNADDWATNGVGRKVSHSYGYGLLDAGAM 327
Score = 77.8 bits (190), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 36/44 (81%), Positives = 40/44 (90%)
Query: 1 GREGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLSTSSATETG 44
GR G GSIFVWASGNGGR+HD+CNCDGYTNSI+TLS SSAT+ G
Sbjct: 174 GRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFG 217
>pdb|1R64|A Chain A, The 2.2 A Crystal Structure Of Kex2 Protease In Complex
With Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid
Inhibitor
pdb|1R64|B Chain B, The 2.2 A Crystal Structure Of Kex2 Protease In Complex
With Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid
Inhibitor
Length = 481
Score = 159 bits (401), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 90/214 (42%), Positives = 128/214 (59%), Gaps = 8/214 (3%)
Query: 58 GVRMLDGDVTDAVEARSLSLNPGHIDIYSASWGPDDDGKTVDGPGELATRAFIEGVTRGR 117
G+R+L GD+T EA SL DIYS SWGP DDG+ + GP +L +A ++GVT GR
Sbjct: 122 GIRILSGDITTEDEAASLIYGLDVNDIYSCSWGPADDGRHLQGPSDLVKKALVKGVTEGR 181
Query: 118 EGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLSTSSATETGQVPWYSEACSSTLATTYS 177
+ KG+I+V+ASGNGG DNCN DGYTNSI++++ + P YSE CS+ +A TYS
Sbjct: 182 DSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSITIGAIDHKDLHPPYSEGCSAVMAVTYS 241
Query: 178 SGSSFEHQVVTTDLHHDCTSNHTGL---APLAAGI--CAWPSRPNPASRGVTCRHIVVAP 232
SGS + ++D++ C+++H G APLAAG+ + PN R V I+ A
Sbjct: 242 SGSG--EYIHSSDINGRCSNSHGGTSAAAPLAAGVYTLLLEANPNLTWRDVQYLSILSAV 299
Query: 233 ARPANLRAPDWATNGVGRNVSHSFGYGLMDATAM 266
N DW + +G+ SH +G+G +DA +
Sbjct: 300 GLEKNADG-DWRDSAMGKKYSHRYGFGKIDAHKL 332
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/36 (63%), Positives = 31/36 (86%)
Query: 1 GREGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLS 36
GR+ KG+I+V+ASGNGG DNCN DGYTNSI++++
Sbjct: 180 GRDSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSIT 215
>pdb|2ID4|A Chain A, The 1.9 A Structure Of Kex2 In Complex With An
Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.
pdb|2ID4|B Chain B, The 1.9 A Structure Of Kex2 In Complex With An
Ac-R-E-R-K-Chloromethyl Ketone Inhibitor
Length = 503
Score = 159 bits (401), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 90/214 (42%), Positives = 128/214 (59%), Gaps = 8/214 (3%)
Query: 58 GVRMLDGDVTDAVEARSLSLNPGHIDIYSASWGPDDDGKTVDGPGELATRAFIEGVTRGR 117
G+R+L GD+T EA SL DIYS SWGP DDG+ + GP +L +A ++GVT GR
Sbjct: 129 GIRILSGDITTEDEAASLIYGLDVNDIYSCSWGPADDGRHLQGPSDLVKKALVKGVTEGR 188
Query: 118 EGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLSTSSATETGQVPWYSEACSSTLATTYS 177
+ KG+I+V+ASGNGG DNCN DGYTNSI++++ + P YSE CS+ +A TYS
Sbjct: 189 DSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSITIGAIDHKDLHPPYSEGCSAVMAVTYS 248
Query: 178 SGSSFEHQVVTTDLHHDCTSNHTGL---APLAAGI--CAWPSRPNPASRGVTCRHIVVAP 232
SGS + ++D++ C+++H G APLAAG+ + PN R V I+ A
Sbjct: 249 SGSG--EYIHSSDINGRCSNSHGGTSAAAPLAAGVYTLLLEANPNLTWRDVQYLSILSAV 306
Query: 233 ARPANLRAPDWATNGVGRNVSHSFGYGLMDATAM 266
N DW + +G+ SH +G+G +DA +
Sbjct: 307 GLEKNADG-DWRDSAMGKKYSHRYGFGKIDAHKL 339
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/36 (63%), Positives = 31/36 (86%)
Query: 1 GREGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLS 36
GR+ KG+I+V+ASGNGG DNCN DGYTNSI++++
Sbjct: 187 GRDSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSIT 222
>pdb|1OT5|A Chain A, The 2.4 Angstrom Crystal Sructure Of Kex2 In Complex With
A Peptidyl- Boronic Acid Inhibitor
pdb|1OT5|B Chain B, The 2.4 Angstrom Crystal Sructure Of Kex2 In Complex With
A Peptidyl- Boronic Acid Inhibitor
Length = 477
Score = 159 bits (401), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 90/214 (42%), Positives = 128/214 (59%), Gaps = 8/214 (3%)
Query: 58 GVRMLDGDVTDAVEARSLSLNPGHIDIYSASWGPDDDGKTVDGPGELATRAFIEGVTRGR 117
G+R+L GD+T EA SL DIYS SWGP DDG+ + GP +L +A ++GVT GR
Sbjct: 120 GIRILSGDITTEDEAASLIYGLDVNDIYSCSWGPADDGRHLQGPSDLVKKALVKGVTEGR 179
Query: 118 EGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLSTSSATETGQVPWYSEACSSTLATTYS 177
+ KG+I+V+ASGNGG DNCN DGYTNSI++++ + P YSE CS+ +A TYS
Sbjct: 180 DSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSITIGAIDHKDLHPPYSEGCSAVMAVTYS 239
Query: 178 SGSSFEHQVVTTDLHHDCTSNHTGL---APLAAGI--CAWPSRPNPASRGVTCRHIVVAP 232
SGS + ++D++ C+++H G APLAAG+ + PN R V I+ A
Sbjct: 240 SGSG--EYIHSSDINGRCSNSHGGTSAAAPLAAGVYTLLLEANPNLTWRDVQYLSILSAV 297
Query: 233 ARPANLRAPDWATNGVGRNVSHSFGYGLMDATAM 266
N DW + +G+ SH +G+G +DA +
Sbjct: 298 GLEKNADG-DWRDSAMGKKYSHRYGFGKIDAHKL 330
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/36 (63%), Positives = 31/36 (86%)
Query: 1 GREGKGSIFVWASGNGGRDHDNCNCDGYTNSIWTLS 36
GR+ KG+I+V+ASGNGG DNCN DGYTNSI++++
Sbjct: 178 GRDSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSIT 213
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 28.9 bits (63), Expect = 2.9, Method: Composition-based stats.
Identities = 26/100 (26%), Positives = 35/100 (35%), Gaps = 14/100 (14%)
Query: 17 GRDHDNCNCDGYTNSIWTLSTSSATETGQKADLTINFSLSPGVRMLDGDVTDAVEARSLS 76
GRD N+ W L + T GQ L N SL + S+
Sbjct: 503 GRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI--------------SVG 548
Query: 77 LNPGHIDIYSASWGPDDDGKTVDGPGELATRAFIEGVTRG 116
+P I + + WG + V ATR F+ GV G
Sbjct: 549 TDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHG 588
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
0.314 0.130 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,335,494
Number of Sequences: 62578
Number of extensions: 408552
Number of successful extensions: 607
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 593
Number of HSP's gapped (non-prelim): 15
length of query: 266
length of database: 14,973,337
effective HSP length: 97
effective length of query: 169
effective length of database: 8,903,271
effective search space: 1504652799
effective search space used: 1504652799
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)