Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate H281DRAFT_01831 H281DRAFT_01831 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >FitnessBrowser__Burk376:H281DRAFT_01831 Length = 414 Score = 292 bits (748), Expect = 1e-83 Identities = 158/381 (41%), Positives = 230/381 (60%), 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: 25 SPIRELFKYLGEPGMISFAGGYPASDLFDVDGLQQAEARAYQDP-NSCLQYGPTDGLPRL 83 Query: 76 RQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAALQVFQL 135 + + L RGV C + + +T+GSQQ LD++ R L+ PGD + E+P Y A LQ +L Sbjct: 84 KHELISLMARRGVPCALNEMLVTTGSQQGLDLLLRVLVSPGDVVFTEQPAYPATLQALKL 143 Query: 136 AQANILSVDTDDDGMLVEQLADLLETTRV---KAVYLVPTFGNPGGKTLSEARRRRLVEL 192 QA I++V D G+ V+ LA+LL + RV K +Y VPTF NP G T++ RR L++L Sbjct: 144 QQAKIVTVPVDAHGLDVDHLAELLASGRVARPKLLYTVPTFANPTGATITRERRIALLKL 203 Query: 193 AKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILAPGMRIGWI 251 A ++ F+I+EDDPYG++ F+ + A E+ G D VV+ ++ SKI+APG+R+GW Sbjct: 204 AVQYKFLIVEDDPYGDLRFSGVAVPSIISLAAEVEGSRDWVVHFASLSKIVAPGLRVGWT 263 Query: 252 VMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALADAL 311 + P + ++ VI KQ DL + +Q I AEYL+ LE + I E Y +KC AL +AL Sbjct: 264 IAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITEMYGRKCEALCEAL 323 Query: 312 ESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRTLR 371 SQ G+ L+F RP GGMF+WAR D ++ +EN V++VPG+AF+ D D +LR Sbjct: 324 RSQFGDTLQFHRPDGGMFVWARIE-GIDASALLQHAIENKVMFVPGKAFFADRIDPASLR 382 Query: 372 LSYSTVSADGLMTAVERLAKS 392 LS++ + +RL ++ Sbjct: 383 LSFAAPGIADIEEGAKRLRRA 403 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: 425 Number of extensions: 20 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: 414 Length adjustment: 31 Effective length of query: 362 Effective length of database: 383 Effective search space: 138646 Effective search space used: 138646 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