Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate Dsui_0883 Dsui_0883 transcriptional regulator with HTH domain and aminotransferase domain
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >FitnessBrowser__PS:Dsui_0883 Length = 475 Score = 158 bits (400), Expect = 3e-43 Identities = 111/365 (30%), Positives = 177/365 (48%), Gaps = 13/365 (3%) Query: 21 IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80 I E+L+ ++ P ++ F P+ +P + R + A + G L Sbjct: 98 IFEILESVKNPAVVPFGSSFASPELYPLDKLGRCLAAAARHLDPR--ATVTDLPPGNEEL 155 Query: 81 REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140 R I RG E++VTSG+ + L + + PG+ + + PT+ LQA Sbjct: 156 RRQIALRYLSRGANVSPQEIVVTSGAMEGLNLCLQAVTRPGDLVAIESPTFYANLQAIER 215 Query: 141 YEPQYLSVPGDA-EGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALLDLCA 198 + + +P EG LAA+E AL Q P K + +F NP ++S AR+ L+ L A Sbjct: 216 LGLKVIEIPTHPREGISLAALEDALRQHPIKACLCMLNFSNPITGSLSDARKAELVALLA 275 Query: 199 KHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWIN 258 ++ VP++ED Y EL Y G+ P+ + R+G VL SFSK++ P R+GW+ Sbjct: 276 RYQVPLIEDDVYAEL-YFGDQAPAHAKAED-RHG----LVLHVSSFSKSLAPGYRIGWVA 329 Query: 259 GPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQN-FDSHIRRLRAGYKERRDAMLTALS 317 G ++ +K L T+ QI L + + +D+H+RRLR + + AM+ A+ Sbjct: 330 G-GRFTQKIQRLKLTTSLATTVPVQIALAEYLKHGGYDNHLRRLRRTFSLQEIAMVGAVE 388 Query: 318 EFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLR 377 PAG +P GG F+W+ELP G D + L R D ++ PG F A R + LR Sbjct: 389 RHFPAGTRLARPSGGYFLWVELPPGVDTL-ALHRLALDQGISIAPGPIFSAKREYGHCLR 447 Query: 378 LSFSN 382 L++ + Sbjct: 448 LNYGH 452 Lambda K H 0.320 0.138 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 473 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 404 Length of database: 475 Length adjustment: 32 Effective length of query: 372 Effective length of database: 443 Effective search space: 164796 Effective search space used: 164796 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory