Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 8501445 DvMF_2175 transcriptional regulator, GntR family with aminotransferase domain (RefSeq)
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >FitnessBrowser__Miya:8501445 Length = 498 Score = 166 bits (420), Expect = 1e-45 Identities = 117/389 (30%), Positives = 190/389 (48%), Gaps = 16/389 (4%) Query: 21 IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80 I +L+ + +++ F PD P A+ R ++ +S +G A Y G L Sbjct: 117 ISTVLEAVGNRDLVPFGVLCPDETLLPGRALGRILSEVMRSRAGEAAA--YATIPGDLEL 174 Query: 81 REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140 R I G+ AG D++L+T+G+ +AL + L PG+ +++ PTY LQ Sbjct: 175 RRQIAWRHRECGVGAGPDDILITNGAVEALYIALRCLTRPGDIVMIQSPTYYCFLQLIES 234 Query: 141 YEPQYLSVPGDAE-GPDLAAVEAALEQ-KPKFFYLVPDFQNPNGTTISLARREALLDLCA 198 + + VP E G D V L++ + P+F NP+G+ + +LD+ A Sbjct: 235 LGLRAIEVPSTPEAGVDPRDVRHILDRHRVAACAFSPNFNNPDGSLTPDDAKREILDMLA 294 Query: 199 KHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWIN 258 + G+ ++ED T+L Y + + D G +T C SFSKT+ P R+GW+ Sbjct: 295 ERGIHLIEDDVSTDLHYGPSRPSTFLQWDVH---GLVT---LCSSFSKTVAPGFRMGWMV 348 Query: 259 GPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQN-FDSHIRRLRAGYKERRDAMLTALS 317 + R +K ++ +T+ Q + + + Q F+ +RRLR + + AM L+ Sbjct: 349 -TGRIGERAREIKATTNVCGATLTQFAMAEYLRQGLFERQLRRLRTAFSRQMQAMRMHLA 407 Query: 318 EFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKNTLR 377 + P+G T+PEGG +W+ELP GTDGV+L RA + A ++ PG+ F N LR Sbjct: 408 DCFPSGTGVTRPEGGGVLWLELPPGTDGVELFFRA-RQAGISVAPGAVFSTQEKFANYLR 466 Query: 378 LSFSNNNPERIREGIR---RLCGLLQTVA 403 L + ER+ EG+R RL G +T A Sbjct: 467 LGCNGLWNERMAEGLRTLGRLAGECRTGA 495 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: 579 Number of extensions: 34 Number of successful extensions: 5 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: 498 Length adjustment: 33 Effective length of query: 371 Effective length of database: 465 Effective search space: 172515 Effective search space used: 172515 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