Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_026607651.1 METAC_RS0114830 branched-chain amino acid aminotransferase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_000427445.1:WP_026607651.1 Length = 287 Score = 130 bits (327), Expect = 4e-35 Identities = 90/277 (32%), Positives = 136/277 (49%), Gaps = 14/277 (5%) Query: 28 EATIPIL---THALHYGTSIFEGIRAYWN-SDNNNLYVFRARDHYVRFHDSAKIMSIKVG 83 E +PI+ THA+ G+S+F+G RA+ + + +L H R + SA M +K Sbjct: 20 EGNVPIMGPRTHAVWLGSSVFDGARAFEGVTPDLDL-------HCARVNQSAGKMHLKPS 72 Query: 84 YSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAIITVPFGHYLEP 143 S + + T E L+ D ++YIRP+ + + + D T +T+ +P Sbjct: 73 VSTETWVGLTKEGLKRFDRSAELYIRPMYWAERNGWLAVAPDPDSTRWCLTLYEVPMPKP 132 Query: 144 KGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLNRDGYVAEGSG 203 G + + R N P++AK +Y N+ AI + + GFD +L + G VAE + Sbjct: 133 DGFSITLSPYRRPTNETMPVEAKAGCLYPNNARAIFETRARGFDNCLLCDMLGNVAELAT 192 Query: 204 ENIFIIKDGILYTPPVYDSILEGITRDTVITIARDLGLTVTEKRITREELYTADEVFFTG 263 NIF+ +DG+L TP + L+GITR VI + R G+ V E + + ADE+F TG Sbjct: 193 ANIFMARDGVLMTPSPNGTFLDGITRRRVIGLLRAAGIEVVETTLRYADFQAADEIFSTG 252 Query: 264 TAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVH 300 +V PV ID R I EPGP K R Y H Sbjct: 253 NYTKVNPVNRIDDRKI---EPGPFYRKARELYWAFAH 286 Lambda K H 0.321 0.139 0.409 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: 236 Number of extensions: 12 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: 314 Length of database: 287 Length adjustment: 27 Effective length of query: 287 Effective length of database: 260 Effective search space: 74620 Effective search space used: 74620 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: 48 (23.1 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