Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate N515DRAFT_1217 N515DRAFT_1217 transcriptional regulator, GntR family
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >FitnessBrowser__Dyella79:N515DRAFT_1217 Length = 468 Score = 182 bits (462), Expect = 2e-50 Identities = 115/379 (30%), Positives = 193/379 (50%), Gaps = 15/379 (3%) Query: 21 IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80 ++E+L +L R +++ P P P AA+ A + + + A L Y +G L Sbjct: 92 LQEVLDMLARSDVLPLHSATPSPALLPQAALTAALSRSLRHHPAA--VLDYAPPQGLPAL 149 Query: 81 REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140 R I + G DE+++T+G+ + + + L PG+ +LV PTY G LQA + Sbjct: 150 RRQIARRYAQLGAAVSPDEIVITAGAMEGISLALRTLAEPGDVVLVETPTYHGILQAVAA 209 Query: 141 YEPQYLSVPG-DAEGPDLAAVEAALEQ-KPKFFYLVPDFQNPNGTTISLARREALLDLCA 198 + L VP +G D+A ++ L+Q + + LVP+F NP G+ A ++ALL CA Sbjct: 210 LRLKVLEVPNLPGQGIDVARLDQLLQQNRVRAAVLVPNFNNPLGSVTGDAAKQALLASCA 269 Query: 199 KHGVPIVEDAAYTELRYEGE-PIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWI 257 +HG ++ED Y +L + GE P P R N++ CGSFSK++ P LR+GWI Sbjct: 270 RHGTVVIEDDVYGDLAWSGERPSP-------LRRWDTRGNLISCGSFSKSLSPGLRLGWI 322 Query: 258 NGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQ-NFDSHIRRLRAGYKERRDAMLTAL 316 A + LV K + +++ Q+ + + + + + + H+RRLR + + A+ Sbjct: 323 AAGAWT-DALVRAKYFSTVGAASLPQLAMAEYLQKHDLERHLRRLRRALADNAQRLHEAI 381 Query: 317 SEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTL 376 S PAG ++P GG+ +W++LPEG DG +L A + + PG F + + L Sbjct: 382 SRHWPAGTRASEPRGGLSLWLQLPEGGDG-QMLFEAALEQGIGTSPGVLFSSRGDYGDCL 440 Query: 377 RLSFSNNNPERIREGIRRL 395 RLS R+ + +++L Sbjct: 441 RLSCGMPWDARLEQALKKL 459 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: 490 Number of extensions: 30 Number of successful extensions: 4 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: 468 Length adjustment: 32 Effective length of query: 372 Effective length of database: 436 Effective search space: 162192 Effective search space used: 162192 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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