Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate YP_428086.1 Rru_A3004 class I and II aminotransferase
Query= reanno::azobra:AZOBR_RS06555 (404 letters) >NCBI__GCF_000013085.1:YP_428086.1 Length = 411 Score = 399 bits (1024), Expect = e-115 Identities = 205/401 (51%), Positives = 268/401 (66%), Gaps = 4/401 (0%) Query: 3 VDWGNVFAGRVAGMGASEIRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSN 62 +DW +A R M ASEIRELLKLL++P+++SFAGGIPDP FPT A AY + Sbjct: 1 MDWKGAYAHRAGAMRASEIRELLKLLDQPDVLSFAGGIPDPTLFPTEAAREAYGAVLGEP 60 Query: 63 SGAGGALQYTISEGFTPLREWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGE 122 +LQY+ISEG+ PLR WI A++ RG+ + +++TSGSQQ L+++GKLLI PG+ Sbjct: 61 GVGPLSLQYSISEGYVPLRRWIVAHMASRGVVCDEENIVITSGSQQGLDYLGKLLISPGD 120 Query: 123 KILVTRPTYLGALQAFSPYEPQYLSVPGDAEGPDLAAV-EAALEQ--KPKFFYLVPDFQN 179 VTRPTYLGALQAF+PYEP+Y + P A EAAL +P Y+VPDF N Sbjct: 121 SAYVTRPTYLGALQAFNPYEPRYADLAFGEGAPTPAQCREAALAAGGRPALAYVVPDFAN 180 Query: 180 PNGTTISLARREALLDLCAKHGVPIVEDAAYTELRYEGEPIPSMVALDAARNGG-KITNV 238 P G T+S R LL+ + GVP+VEDAAY LRY G I S +ALD AR G + V Sbjct: 181 PTGETLSREDRLRLLEHVSALGVPLVEDAAYAALRYAGADIASCLALDIARVGDIDHSRV 240 Query: 239 LFCGSFSKTMVPALRVGWINGPAEVINRLVLMKQAGDLHTSTINQIVLHDVVSQNFDSHI 298 ++CGSFSKT+ P LRVGWI +++ ++VL KQA DLH++TINQ+V+H + +D + Sbjct: 241 IYCGSFSKTIAPGLRVGWICAARDLVQKVVLTKQAADLHSATINQMVMHRLAEAIYDEQV 300 Query: 299 RRLRAGYKERRDAMLTALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANV 358 +++ Y RRDA+L AL++F P GV+WT PEGGMFVW+ LP DG +LLA +++D V Sbjct: 301 KKIIGVYAARRDALLAALAKFMPEGVSWTAPEGGMFVWVTLPANIDGAELLAESLRDERV 360 Query: 359 AFVPGSAFHADRSGKNTLRLSFSNNNPERIREGIRRLCGLL 399 AFVPG AF D SG NTLRL+FS + I EGI RL L+ Sbjct: 361 AFVPGGAFFFDGSGANTLRLNFSLPSEAVINEGIARLARLI 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: 539 Number of extensions: 22 Number of successful extensions: 3 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: 411 Length adjustment: 31 Effective length of query: 373 Effective length of database: 380 Effective search space: 141740 Effective search space used: 141740 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