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= psy3461
(87 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2AEX|A Chain A, The 1.58a Crystal Structure Of Human Coproporphyrinogen
Oxidase Reveals The Structural Basis Of Hereditary
Coproporphyria
Length = 346
Score = 127 bits (319), Expect = 2e-30, Method: Composition-based stats.
Identities = 55/84 (65%), Positives = 71/84 (84%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
VKK+ D + E+ WQ LRRGRYVEFNL+YDRGTKFGL TPG+R ESILMSLPLTA+WE
Sbjct: 261 VKKHCDDSFTPQEKLWQQLRRGRYVEFNLLYDRGTKFGLFTPGSRIESILMSLPLTARWE 320
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
YMH+P E SKE +++++L++P++W
Sbjct: 321 YMHSPSENSKEAEILEVLRHPRDW 344
>pdb|1TKL|A Chain A, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
pdb|1TKL|B Chain B, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
pdb|1TLB|A Chain A, Yeast Coproporphyrinogen Oxidase
pdb|1TLB|D Chain D, Yeast Coproporphyrinogen Oxidase
pdb|1TLB|Q Chain Q, Yeast Coproporphyrinogen Oxidase
pdb|1TLB|S Chain S, Yeast Coproporphyrinogen Oxidase
pdb|1TLB|U Chain U, Yeast Coproporphyrinogen Oxidase
pdb|1TLB|W Chain W, Yeast Coproporphyrinogen Oxidase
Length = 326
Score = 110 bits (276), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 51/84 (60%), Positives = 63/84 (75%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
VK+ KD Y E+QWQ +RRGRYVEFNLIYDRGT+FGL+TPG+R ESILMSLP A W
Sbjct: 241 VKRRKDMPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILMSLPEHASWL 300
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y H P S+E +L+++ P+EW
Sbjct: 301 YNHHPAPGSREAKLLEVTTKPREW 324
>pdb|1TXN|A Chain A, Crystal Structure Of Coproporphyrinogen Iii Oxidase
pdb|1TXN|B Chain B, Crystal Structure Of Coproporphyrinogen Iii Oxidase
Length = 328
Score = 108 bits (269), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 50/84 (59%), Positives = 62/84 (73%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
VK+ KD Y E+QWQ +RRGRYVEFNLIYDRGT+FGL+TPG+R ESIL SLP A W
Sbjct: 243 VKRRKDXPYTKEEQQWQAIRRGRYVEFNLIYDRGTQFGLRTPGSRVESILXSLPEHASWL 302
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y H P S+E +L+++ P+EW
Sbjct: 303 YNHHPAPGSREAKLLEVTTKPREW 326
>pdb|3DWR|A Chain A, Leishmania Major Coproporphyrinogen Iii Oxidase With Bound
Ligand
pdb|3DWR|B Chain B, Leishmania Major Coproporphyrinogen Iii Oxidase With Bound
Ligand
Length = 309
Score = 79.0 bits (193), Expect = 7e-16, Method: Composition-based stats.
Identities = 39/84 (46%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
V + K+ Y + ++Q RRGRY EFNL+ DRGTKFGLQ+ G R ESIL+SLP A+W
Sbjct: 226 VNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQS-GGRTESILISLPPRARWG 284
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y PE + E +L + ++W
Sbjct: 285 YNWQPEPGTPEARLTEYFLTKRQW 308
>pdb|1VJU|A Chain A, Coproporphyrinogen Iii Oxidase From Leishmania Major
pdb|1VJU|B Chain B, Coproporphyrinogen Iii Oxidase From Leishmania Major
pdb|2QT8|A Chain A, Coproporphyrinogen Iii Oxidase From Leishmania Major
pdb|2QT8|B Chain B, Coproporphyrinogen Iii Oxidase From Leishmania Major
pdb|3DWS|A Chain A, Leishmania Major Coproporphyrinogen Iii Oxidase With Bound
Ligand
pdb|3DWS|B Chain B, Leishmania Major Coproporphyrinogen Iii Oxidase With Bound
Ligand
Length = 309
Score = 79.0 bits (193), Expect = 7e-16, Method: Composition-based stats.
Identities = 39/84 (46%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
V + K+ Y + ++Q RRGRY EFNL+ DRGTKFGLQ+ G R ESIL+SLP A+W
Sbjct: 226 VNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQS-GGRTESILISLPPRARWG 284
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y PE + E +L + ++W
Sbjct: 285 YNWQPEPGTPEARLTEYFLTKRQW 308
>pdb|3E8J|A Chain A, Coproporphyrinogen Iii Oxidase From Leishmania Naiffi
pdb|3E8J|B Chain B, Coproporphyrinogen Iii Oxidase From Leishmania Naiffi
Length = 306
Score = 78.6 bits (192), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 41/84 (48%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
V + K+ Y + ++Q RRGRY EFNL+ DRGTKFGLQ+ G R ESILMSLP A+W
Sbjct: 223 VNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQS-GGRTESILMSLPPRARWG 281
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y PE + E +L + K+W
Sbjct: 282 YNWHPEPGTPEARLTEYFLTKKQW 305
>pdb|3EJO|A Chain A, Coproporphyrinogen Iii Oxidase From Leishmania Donovani
pdb|3EJO|B Chain B, Coproporphyrinogen Iii Oxidase From Leishmania Donovani
Length = 310
Score = 77.4 bits (189), Expect = 2e-15, Method: Composition-based stats.
Identities = 39/84 (46%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAKWE 63
V + K+ Y + ++Q RRGRY EFNL+ DRGTKFGLQ+ G R ESIL+SLP A+W
Sbjct: 227 VNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQS-GGRTESILISLPPRARWG 285
Query: 64 YMHTPEETSKEGQLIKILKNPKEW 87
Y PE + E +L + ++W
Sbjct: 286 YDWQPEPGTPEARLTEYFLMKRQW 309
>pdb|1TK1|A Chain A, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
Length = 260
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 4 VKKNKDAGYGYHERQWQLLRRGR 26
VK+ KD Y E+QWQ +RRGR
Sbjct: 238 VKRRKDMPYTKEEQQWQAIRRGR 260
>pdb|1SPX|A Chain A, Crystal Structure Of Glucose Dehydrogenase Of
Caenorhabditis Elegans In The Apo-Form
Length = 278
Score = 26.9 bits (58), Expect = 3.1, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 18/41 (43%)
Query: 34 YDRGTKFGLQTPGARYESILMSLPLTAKWEYMHTPEETSKE 74
Y R T L G R SI L T M PEETSK+
Sbjct: 172 YTRNTAIDLIQHGIRVNSISPGLVATGFGSAMGMPEETSKK 212
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 12/56 (21%)
Query: 6 KNKDAGYGYHERQWQLLRRGRYVEFNLIYDRGTKFGLQTPGARYESILMSLPLTAK 61
K K G+G +R+ ++LRR K GL TPG E L L L K
Sbjct: 928 KRKGEGFGVDKREVEVLRRAE------------KLGLVTPGKTPEEQLKELFLQGK 971
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
0.318 0.137 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,086,635
Number of Sequences: 62578
Number of extensions: 111451
Number of successful extensions: 188
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 172
Number of HSP's gapped (non-prelim): 12
length of query: 87
length of database: 14,973,337
effective HSP length: 55
effective length of query: 32
effective length of database: 11,531,547
effective search space: 369009504
effective search space used: 369009504
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)