Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate YP_002826484.1 NGR_c19680 aminotransferase
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000018545.1:YP_002826484.1 Length = 408 Score = 432 bits (1111), Expect = e-126 Identities = 221/402 (54%), Positives = 284/402 (70%), Gaps = 6/402 (1%) Query: 3 VDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSN 62 ++W ++FA R + M ASEIRELLKLL+RP+IISFAGGIPDP+ FP A ++AY +IF Sbjct: 2 LNWESIFATRSSRMKASEIRELLKLLDRPDIISFAGGIPDPELFPQAEFSQAYAEIF-GG 60 Query: 63 SGAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGE 122 ALQY++SEG+ PLREW+ + GI A +D + +TSGSQQ L+++GKL + P + Sbjct: 61 PAVSAALQYSVSEGYRPLREWLAKQMAALGIPATVDNIFITSGSQQGLDYLGKLFLSPRD 120 Query: 123 KILVTRPTYLGALQAFSPYEPQYLSV-PGDAEGPDLAAVEAALEQ--KPKFFYLVPDFQN 179 LVT PTYLGALQAF+ YEP Y + PG P+ A V+ A E + KF YL DF N Sbjct: 121 TALVTWPTYLGALQAFNAYEPNYDRLNPGGNRTPE-AYVQTAAEAGGRVKFAYLSADFAN 179 Query: 180 PNGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGG-KITNV 238 P G T+ A RE +LDL + G+P++EDAAY LRY+GE IP ++AL+ AR G Sbjct: 180 PTGETVDRAGRERVLDLAEELGIPVIEDAAYQSLRYDGEAIPPILALEIARKGDINSART 239 Query: 239 LFCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHI 298 ++CGSFSKT+ P LRVGW+ VI +LVL+KQA DLH+STINQ+ + V + FD + Sbjct: 240 IYCGSFSKTLAPGLRVGWVCAAEPVIRKLVLLKQAADLHSSTINQMAICTVAGRGFDEQV 299 Query: 299 RRLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANV 358 ++ A YK RRDAML AL + PAGVTWTKPEGGMFVW+ LP+GTDG +LLA++I+ A V Sbjct: 300 AKIHAVYKHRRDAMLAALDRYMPAGVTWTKPEGGMFVWVTLPKGTDGAELLAKSIQSAKV 359 Query: 359 AFVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLLQ 400 AFVPG AF AD SG+NTLRLSFS N + I EGIRRL L++ Sbjct: 360 AFVPGRAFFADGSGENTLRLSFSCANDKMIEEGIRRLGDLIR 401 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: 531 Number of extensions: 15 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: 408 Length adjustment: 31 Effective length of query: 373 Effective length of database: 377 Effective search space: 140621 Effective search space used: 140621 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 10 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