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= 029322
(195 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 37/98 (37%), Positives = 51/98 (52%), Gaps = 8/98 (8%)
Query: 46 KSLKNRRLQNWGGVVH-EKGLLPQDLP--PWLTMITRRIYEK---SGLFPSAINHILINE 99
KSLK+RR++++G H E + +D P L I EK G + + IN+
Sbjct: 145 KSLKHRRVKHFGYEFHYENNNVDKDKPLSGGLPDICESFLEKWLRKGYIKHKPDQMTINQ 204
Query: 100 YQPNQGIMPHQDGPAYFP-VVAILSLGSPVVMDFTPHP 136
Y+P QGI H D + F + LSLGS +VMDF HP
Sbjct: 205 YEPGQGIPAHIDTHSAFEDEIVSLSLGSEIVMDFK-HP 241
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing Trna
Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 36/98 (36%), Positives = 49/98 (50%), Gaps = 8/98 (8%)
Query: 46 KSLKNRRLQNWGGVVH-EKGLLPQDLP--PWLTMITRRIYEK---SGLFPSAINHILINE 99
KSLK+RR++++G H E + +D P L I EK G + IN+
Sbjct: 145 KSLKHRRVKHFGYEFHYENNNVDKDKPLSGGLPDICESFLEKWLRKGYIKHKPDQXTINQ 204
Query: 100 YQPNQGIMPHQDGPAYFP-VVAILSLGSPVVMDFTPHP 136
Y+P QGI H D + F + LSLGS +V DF HP
Sbjct: 205 YEPGQGIPAHIDTHSAFEDEIVSLSLGSEIVXDFK-HP 241
>pdb|4F9D|A Chain A, Structure Of Escherichia Coli Pgab 42-655 In Complex With
Nickel
pdb|4F9D|B Chain B, Structure Of Escherichia Coli Pgab 42-655 In Complex With
Nickel
Length = 618
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 40/90 (44%)
Query: 5 ENFNQFTVGNLPTLMYVADFITNIEETQLLNNIYGAPLSKWKSLKNRRLQNWGGVVHEKG 64
++++ + +P L VA+ + QL N I P +K KS+ + QNW +
Sbjct: 525 KSYDWTAIMAMPYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAQNWQKNGQHQA 584
Query: 65 LLPQDLPPWLTMITRRIYEKSGLFPSAINH 94
+ Q L W++++ + G +P H
Sbjct: 585 ISSQQLAHWMSLLQLNGVKNYGYYPDNFLH 614
>pdb|4F9J|A Chain A, Structure Of Escherichia Coli Pgab 42-655 In Complex With
Iron
pdb|4F9J|B Chain B, Structure Of Escherichia Coli Pgab 42-655 In Complex With
Iron
Length = 618
Score = 31.2 bits (69), Expect = 0.39, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 33/79 (41%)
Query: 16 PTLMYVADFITNIEETQLLNNIYGAPLSKWKSLKNRRLQNWGGVVHEKGLLPQDLPPWLT 75
P L VA+ + QL N I P +K KS+ + QNW + + Q L W +
Sbjct: 536 PYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAQNWQKNGQHQAISSQQLAHWXS 595
Query: 76 MITRRIYEKSGLFPSAINH 94
++ + G +P H
Sbjct: 596 LLQLNGVKNYGYYPDNFLH 614
>pdb|3O1M|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1O|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1P|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1R|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1S|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1T|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1U|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
pdb|3O1V|A Chain A, Iron-Catalyzed Oxidation Intermediates Captured In A Dna
Repair Dioxygenase
Length = 206
Score = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 58 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 117
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 118 LCLHQDKDEPDLRAPIVSVSLGLPAIFQF 146
>pdb|3BIE|A Chain A, X-Ray Structure Of E Coli Alkb Bound To Dsdna Containing
1meaT WITH Mn And 2kg
Length = 202
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 56 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 115
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 116 LCLHQDKDEPDLRAPIVSVSLGLPAIFQF 144
>pdb|3BI3|A Chain A, X-Ray Structure Of Alkb Protein Bound To Dsdna Containing
1meaA WITH Cofactors
Length = 201
Score = 30.4 bits (67), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 56 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 115
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 116 LCLHQDKDEPDLRAPIVSVSLGLPAIFQF 144
>pdb|3KHC|A Chain A, Crystal Structure Of Escherichia Coli Alkb In Complex With
Ssdna Containing A 1-Methylguanine Lesion
pdb|3KHC|B Chain B, Crystal Structure Of Escherichia Coli Alkb In Complex With
Ssdna Containing A 1-Methylguanine Lesion
Length = 219
Score = 30.0 bits (66), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 36/90 (40%), Gaps = 15/90 (16%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 71 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 130
Query: 106 IMPHQDGPA---YFPVVAILSLGSPVVMDF 132
+ HQD P+V++ SLG P + F
Sbjct: 131 LSLHQDKAEPDLRAPIVSV-SLGLPAIFQF 159
>pdb|3KHB|A Chain A, Crystal Structure Of Escherichia Coli Alkb With Co(Ii) And
2-Og
pdb|3KHB|B Chain B, Crystal Structure Of Escherichia Coli Alkb With Co(Ii) And
2-Og
Length = 219
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 71 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 130
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 131 LSLHQDKDEPDLRAPIVSVSLGLPAIFQF 159
>pdb|2FD8|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDF|A Chain A, Crystal Structure Of Alkb In Complex With Co(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDG|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
Succinate, And Methylated Trinucleotide T-Mea-T
pdb|2FDH|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
pdb|2FDI|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate, And Methylated Trinucleotide T-Mea-T
(Air 3 Hours)
pdb|2FDJ|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii) And
Succinate
pdb|2FDK|A Chain A, Crystal Structure Of Alkb In Complex With Fe(ii),
2-oxoglutarate, And Methylated Trinucleotide T-mea-t
(air 9 Days)
pdb|3I2O|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mea-T
pdb|3I3M|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mec-T
pdb|3I3Q|A Chain A, Crystal Structure Of Alkb In Complex With Mn(Ii) And
2-Oxoglutarate
pdb|3I3Q|B Chain B, Crystal Structure Of Alkb In Complex With Mn(Ii) And
2-Oxoglutarate
pdb|3I49|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Ii),
2-Oxoglutarate And Methylated Trinucleotide T-Mec-T
Length = 211
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 58 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 117
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 118 LSLHQDKDEPDLRAPIVSVSLGLPAIFQF 146
>pdb|3T3Y|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Iii) And
2-(3- Hydroxypicolinomido)acetic Acid
pdb|3T4H|B Chain B, Crystal Structure Of Alkb In Complex With Fe(Iii) And
N-Oxalyl-S-(3- Nitrobenzyl)-L-Cysteine
pdb|3T4V|A Chain A, Crystal Structure Of Alkb In Complex With Fe(Iii) And
N-Oxalyl-S-(2- Napthalenemethyl)-L-Cysteine
Length = 206
Score = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 58 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 117
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 118 LSLHQDKDEPDLRAPIVSVSLGLPAIFQF 146
>pdb|3BKZ|A Chain A, X-Ray Structure Of E Coli Alkb Crosslinked To Dsdna In The
Active Site
Length = 201
Score = 29.6 bits (65), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 57 GGVVHEKGLL-----PQDLPPWLTM------ITRRIYEKSGLFPSAINHILINEYQPNQG 105
G H +G L PQ PW M + +R +G + LIN Y P
Sbjct: 55 GWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAK 114
Query: 106 IMPHQDG--PAYFPVVAILSLGSPVVMDF 132
+ HQD P + +SLG P + F
Sbjct: 115 LSLHQDKCEPDLRAPIVSVSLGLPAIFQF 143
>pdb|3RHW|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RI5|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RIA|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIF|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate
Length = 347
Score = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 40/157 (25%), Positives = 66/157 (42%), Gaps = 17/157 (10%)
Query: 16 PTLMYVADFITNIEETQLLNNIYGAPLSKWKSLKNRRLQNWGGVVHEKGLLPQDLPPWLT 75
P ++ V + I + ++N Y A L+ +S ++RL GV KG D P
Sbjct: 27 PVVVSVNMLLRTISKIDVVNMEYSAQLTLRESWIDKRLSY--GV---KG----DGQPDFV 77
Query: 76 MIT--RRIYEKSGLFPSAINHILINEYQPNQGIMPHQDGPAYFPVVAILSLGSPVVMDFT 133
++T +I+ FP+ +PN I H DG + V L L P+ + +
Sbjct: 78 ILTVGHQIWMPDTFFPNEKQAYKHTIDKPNVLIRIHNDGTVLYSVRISLVLSCPMYLQYY 137
Query: 134 PHPKLKNNIIPESSNGDAFVTEKNE--WKDSHHPFSI 168
P + +I S A+ T+ E WK+ H P +
Sbjct: 138 PMDVQQCSIDLASY---AYTTKDIEYLWKE-HSPLQL 170
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
0.320 0.139 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,532,795
Number of Sequences: 62578
Number of extensions: 277860
Number of successful extensions: 584
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 24
length of query: 195
length of database: 14,973,337
effective HSP length: 94
effective length of query: 101
effective length of database: 9,091,005
effective search space: 918191505
effective search space used: 918191505
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: 49 (23.5 bits)