Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate H281DRAFT_01667 H281DRAFT_01667 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >FitnessBrowser__Burk376:H281DRAFT_01667 Length = 409 Score = 287 bits (735), Expect = 3e-82 Identities = 155/381 (40%), Positives = 227/381 (59%), Gaps = 6/381 (1%) Query: 16 SAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAFQYGLTEGYPPL 75 S +REL K+ PG+IS GG PA +LFD +GL A ++ N QYG T+G P L Sbjct: 14 SPIRELFKYLAEPGMISFAGGYPASDLFDVDGLASAQKRAYRNS-NRCLQYGPTDGLPEL 72 Query: 76 RQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAALQVFQL 135 + + L RGV C + +T+GSQQ LD++ R L+ PGD +V E+P Y A LQ +L Sbjct: 73 KSELVNLMARRGVTCEPGELLVTTGSQQGLDLLLRVLVAPGDVVVTEQPAYPATLQALKL 132 Query: 136 AQANILSVDTDDDGMLVEQLADLLET---TRVKAVYLVPTFGNPGGKTLSEARRRRLVEL 192 A I++ D G+ VE LA LE+ R K +Y VPTF NP G T++ RR L++L Sbjct: 133 QHAQIVTAQVDGHGIDVENLAAHLESGAVPRPKLLYTVPTFANPTGATITRERRIELLKL 192 Query: 193 AKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILAPGMRIGWI 251 A K+ FVI+EDDPYG++ F+ + + E+ G D VV+ ++ SKI+APG+R+GW Sbjct: 193 AVKYRFVIVEDDPYGDLRFSGDTVPSILALTAEVEGSRDWVVHFASLSKIVAPGVRVGWS 252 Query: 252 VMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALADAL 311 + P + ++ VI KQ DL + +Q I AEYL+ LE + I YR+KC AL + L Sbjct: 253 IAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITTTYRRKCDALCNEL 312 Query: 312 ESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRTLR 371 QL + ++F +P+GGMF+WAR D+ E + +EN V++VPG+AF+ D D +LR Sbjct: 313 RWQLDDAIQFHQPEGGMFVWARIE-GIDSSELLWHAIENKVIFVPGKAFFADKLDVASLR 371 Query: 372 LSYSTVSADGLMTAVERLAKS 392 LS++ + + RL ++ Sbjct: 372 LSFAAPGVEEIQEGARRLKRA 392 Lambda K H 0.320 0.136 0.395 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: 409 Number of extensions: 18 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: 393 Length of database: 409 Length adjustment: 31 Effective length of query: 362 Effective length of database: 378 Effective search space: 136836 Effective search space used: 136836 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: 50 (23.9 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