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= 040691
(585 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MVB|O Chain O, Crystal Structure Of A Triple Rfy Mutant Of Human Mterf1
Bound To The Termination Sequence
Length = 343
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 65/147 (44%), Gaps = 28/147 (19%)
Query: 178 LCNYGFARKKIGMIYKEATEVFRYDFGVLRSKLQAFEKLGLS------QSFVRKVIVRNP 231
L + G RK + + A F + + ++ + GLS FVRK+I +NP
Sbjct: 130 LYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNP 189
Query: 232 KFLVGD-----VNLEFIK---------VLEILKSMGIEFSWIGEHSTEQSTFNWR-TMFS 276
L+ N+EF++ +L ++ G E + + +S N + +FS
Sbjct: 190 AILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDAARRSYANIKEKLFS 249
Query: 277 FLSFCSKIGCSEEQLRILIRQHPEILF 303
+GC+EE+++ + +P+++F
Sbjct: 250 -------LGCTEEEVQKFVLSYPDVIF 269
>pdb|3N6S|A Chain A, Crystal Structure Of Human Mitochondrial Mterf In Complex
With A 15- Mer Dna Encompassing The Trnaleu(Uur) Binding
Sequence
Length = 353
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 64/147 (43%), Gaps = 28/147 (19%)
Query: 178 LCNYGFARKKIGMIYKEATEVFRYDFGVLRSKLQAFEKLGLS------QSFVRKVIVRNP 231
L + G RK + + A F + + ++ + GLS FVRK+I +NP
Sbjct: 131 LYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNP 190
Query: 232 KFLVGD-----VNLEFIK---------VLEILKSMGIEFSWIGEHSTEQSTFNWR-TMFS 276
L+ N+EF++ +L ++ G E + +S N + +FS
Sbjct: 191 FILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFS 250
Query: 277 FLSFCSKIGCSEEQLRILIRQHPEILF 303
+GC+EE+++ + +P+++F
Sbjct: 251 -------LGCTEEEVQKFVLSYPDVIF 270
>pdb|3MVA|O Chain O, Crystal Structure Of Human Mterf1 Bound To The Termination
Sequence
Length = 343
Score = 37.0 bits (84), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 64/147 (43%), Gaps = 28/147 (19%)
Query: 178 LCNYGFARKKIGMIYKEATEVFRYDFGVLRSKLQAFEKLGLS------QSFVRKVIVRNP 231
L + G RK + + A F + + ++ + GLS FVRK+I +NP
Sbjct: 130 LYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNP 189
Query: 232 KFLVGD-----VNLEFIK---------VLEILKSMGIEFSWIGEHSTEQSTFNWR-TMFS 276
L+ N+EF++ +L ++ G E + +S N + +FS
Sbjct: 190 FILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFS 249
Query: 277 FLSFCSKIGCSEEQLRILIRQHPEILF 303
+GC+EE+++ + +P+++F
Sbjct: 250 -------LGCTEEEVQKFVLSYPDVIF 269
>pdb|3N7Q|A Chain A, Crystal Structure Of Human Mitochondrial Mterf Fragment
(Aa 99-399) In Complex With A 12-Mer Dna Encompassing
The Trnaleu(Uur) Binding Sequence
Length = 310
Score = 36.2 bits (82), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 33/147 (22%), Positives = 64/147 (43%), Gaps = 28/147 (19%)
Query: 178 LCNYGFARKKIGMIYKEATEVFRYDFGVLRSKLQAFEKLGLS------QSFVRKVIVRNP 231
L + G RK + + A F + + ++ + GLS FVRK+I +NP
Sbjct: 88 LYSVGLTRKCLCRLLTNAPRTFSNSLDLNKQMVEFLQAAGLSLGHNDPADFVRKIIFKNP 147
Query: 232 KFLVGD-----VNLEFIK---------VLEILKSMGIEFSWIGEHSTEQSTFNWR-TMFS 276
L+ N+EF++ +L ++ G E + +S N + +FS
Sbjct: 148 FILIQSTKRVKANIEFLRSTFNLNSEELLVLICGPGAEILDLSNDYARRSYANIKEKLFS 207
Query: 277 FLSFCSKIGCSEEQLRILIRQHPEILF 303
+GC+EE+++ + +P+++F
Sbjct: 208 -------LGCTEEEVQKFVLSYPDVIF 227
>pdb|3M66|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 270
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 20/115 (17%)
Query: 436 FLLEVGFEENS---------KQFETALKDLRTRARDLRERFDLIVEAGLERKDVCDMVRV 486
FL +VG E+N F L++L+TR L + + DV MVR
Sbjct: 47 FLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSK-------NFSKADVAQMVRK 99
Query: 487 APLILKQKKEVLKTKIDYFVNDFGYPISSLKP----FPQYLMYNMKTVKCRLSMY 537
AP +L E L ++ +F + + + P+ L +++ VK + +Y
Sbjct: 100 APFLLNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVY 154
>pdb|3OPG|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Termination Factor 3
Length = 298
Score = 32.0 bits (71), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 20/115 (17%)
Query: 436 FLLEVGFEENS---------KQFETALKDLRTRARDLRERFDLIVEAGLERKDVCDMVRV 486
FL +VG E+N F L++L+TR L + + DV MVR
Sbjct: 75 FLKDVGIEDNQLGAFLTKNHAIFSEDLENLKTRVAYLHSK-------NFSKADVAQMVRK 127
Query: 487 APLILKQKKEVLKTKIDYFVNDFGYPISSLKP----FPQYLMYNMKTVKCRLSMY 537
AP +L E L ++ +F + + + P+ L +++ VK + +Y
Sbjct: 128 APFLLNFSVERLDNRLGFFQKELELSVKKTRDLVVRLPRLLTGSLEPVKENMKVY 182
>pdb|3GBD|A Chain A, Crystal Structure Of The Isomaltulose Synthase Smua From
Protaminobacter Rubrum
pdb|3GBE|A Chain A, Crystal Structure Of The Isomaltulose Synthase Smua From
Protaminobacter Rubrum In Complex With The Inhibitor
Deoxynojirimycin
Length = 558
Score = 32.0 bits (71), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 235 VGDVNLEFIKVLEILKSMGIEFSWIGEHSTEQSTFNWRTMFSFLSFCSKIGCSEEQLRIL 294
+GD+N I+ L+ LK++GI+ WI H +T N + + + G E+ R++
Sbjct: 27 IGDIN-GIIEKLDYLKALGIDAIWINPHYDSPNTDNGYDIRDYRKIMKEYGTMEDFDRLI 85
>pdb|1M53|A Chain A, Crystal Structure Of Isomaltulose Synthase (Pali) From
Klebsiella Sp. Lx3
Length = 570
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 235 VGDVNLEFIKVLEILKSMGIEFSWIGEHSTEQSTFNWRTMFSFLSFCSKIGCSEE 289
+GD+ I+ L+ LKS+GI+ WI H +T N + ++ + G E+
Sbjct: 41 IGDIR-GIIEKLDYLKSLGIDAIWINPHYDSPNTDNGYDISNYRQIMKEYGTMED 94
>pdb|2RN7|A Chain A, Nmr Solution Structure Of Tnpe Protein From Shigella
Flexneri. Northeast Structural Genomics Target Sfr125
Length = 108
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 271 WRTMFSFLSFCSKIGCSEEQLRILIRQHPEILFEDSGNM 309
W T+ S KIGC+ E LR+ +RQH D G +
Sbjct: 30 WATI---CSIAPKIGCTPETLRVWVRQHERDTGGDDGGL 65
>pdb|2C7T|A Chain A, Crystal Structure Of The Plp-Bound Form Of Btrr, A Dual
Functional Aminotransferase Involved In Butirosin
Biosynthesis.
pdb|2C81|A Chain A, Crystal Structures Of The Plp- And Pmp-Bound Forms Of
Btrr, A Dual Functional Aminotransferase Involved In
Butirosin Biosynthesis
Length = 418
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 17/119 (14%)
Query: 36 GSFYFVQNPRLYRTKKIVKPDNDAYCDVSS-----------GGDVSKVPIATREAQAALL 84
G +NPRL+ + ++ D+ YCD SS GD+ E Q+A+L
Sbjct: 199 GGIIVTKNPRLFELIQQLRADSRVYCDDSSELMHGDMQLVKKGDIQGSNYCLSEFQSAIL 258
Query: 85 EYLHSTRNLQFLDAEH-MSKNSPYFLEKILNKVGNDNEENIGRAITRFFRYHPVNEFEP 142
LQ LD ++ + + + FL L+K+ ++R Y V F+P
Sbjct: 259 -----LDQLQELDDKNAIREKNAMFLNDALSKIDGIKVMKRPPQVSRQTYYGYVFRFDP 312
>pdb|3FF0|A Chain A, Crystal Structure Of A Phenazine Biosynthesis-Related
Protein (Phzb2) From Pseudomonas Aeruginosa At 1.90 A
Resolution
pdb|3FF0|B Chain B, Crystal Structure Of A Phenazine Biosynthesis-Related
Protein (Phzb2) From Pseudomonas Aeruginosa At 1.90 A
Resolution
Length = 163
Score = 29.6 bits (65), Expect = 4.5, Method: Composition-based stats.
Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 17/105 (16%)
Query: 441 GFEE----NSKQFETALKDLRTRARDLRERFDLIVEAGLERKDVCDMVRVAPLILKQKKE 496
GFE+ K ET +K T+ +D R +L VE G D +P++++ K +
Sbjct: 10 GFEDAVELRRKNRETVVKYXNTKGQDRLRRHELFVEDGCGGLWTTDTG--SPIVIRGKDK 67
Query: 497 VLKTKIDYFVNDFGYPISSLKPFPQYLMYNMKTVKCRLSMYNWLK 541
+ + + + SLK FP + YN+K + + W++
Sbjct: 68 LAE-----------HAVWSLKCFPDWEWYNIKVFETDDPNHFWVE 101
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
0.324 0.139 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,141,569
Number of Sequences: 62578
Number of extensions: 624879
Number of successful extensions: 1896
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1885
Number of HSP's gapped (non-prelim): 17
length of query: 585
length of database: 14,973,337
effective HSP length: 104
effective length of query: 481
effective length of database: 8,465,225
effective search space: 4071773225
effective search space used: 4071773225
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 bits)