Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate BPHYT_RS32640 BPHYT_RS32640 2-aminoadipate aminotransferase
Query= reanno::Koxy:BWI76_RS24235 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS32640 Length = 398 Score = 299 bits (765), Expect = 1e-85 Identities = 155/383 (40%), Positives = 236/383 (61%), Gaps = 6/383 (1%) Query: 16 SAVRELLKHSKLPGVISLGGGIPAPELFDTEGLNLAVQQVMNGRFNDAFQYGLTEGYPPL 75 S +REL K+ PG+IS GG PA +LFD EGL+ A + QYG T+G P L Sbjct: 14 SPIRELFKYLAQPGMISFAGGYPASDLFDREGLDAAASRASQ-HATLCLQYGPTDGLPVL 72 Query: 76 RQAVSELCQARGVACPASHVYITSGSQQSLDIVARTLLDPGDAIVVERPTYLAALQVFQL 135 ++ ++ L RGV+C + T+GSQQ D++ R ++ PGD ++VE+P Y A LQ L Sbjct: 73 KEQLAHLMARRGVSCTPQDMLATTGSQQGFDLLLRVMVAPGDVVLVEQPAYPATLQALTL 132 Query: 136 AQANILSVDTDDDGMLVEQLADLLETTRV----KAVYLVPTFGNPGGKTLSEARRRRLVE 191 +A+++++ D DG+ ++ LA LL++ + K +Y VPTF NP G TLS RR L++ Sbjct: 133 QEADVVTIPVDQDGLDIDALAALLDSGTLRRAPKLLYTVPTFANPTGATLSFERRTALLK 192 Query: 192 LAKKHDFVIIEDDPYGEISFTDEVRRPLYQYAVEL-GCEDQVVYTSTFSKILAPGMRIGW 250 LA +H F+I+EDDPYG++ FT L + ++ G D VV+ S+ SKI+APG+R+GW Sbjct: 193 LAARHRFLIVEDDPYGDLRFTGAALPSLLALSEQVPGSRDWVVHFSSLSKIVAPGLRVGW 252 Query: 251 IVMPDWLAQQTVIVKQAADLHTNMLSQVITAEYLSMNRLESQIALIREDYRKKCVALADA 310 ++ + ++ V+ KQ DL ++ +Q I AEYL+ LE + I + Y KC L DA Sbjct: 253 MLAHAEILRRCVVAKQTVDLCSSPWTQAIAAEYLASGALERHLPRIVDAYAVKCRTLCDA 312 Query: 311 LESQLGEHLEFSRPKGGMFLWARFRYPFDTMEWMKKTLENGVVYVPGEAFYNDNPDTRTL 370 LE+QL E + F RP GGMF+WAR + + ++++ +E V++VPG AFY DN D+ L Sbjct: 313 LEAQLAEQIAFHRPAGGMFVWARLKAGQNASDYLRACIERNVMFVPGVAFYKDNIDSSAL 372 Query: 371 RLSYSTVSADGLMTAVERLAKSL 393 RLS++ + T V+R+ ++L Sbjct: 373 RLSFAAPGIADIETGVQRMKQAL 395 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: 407 Number of extensions: 17 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: 393 Length of database: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 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