Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_043795594.1 ALVIN_RS09555 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000025485.1:WP_043795594.1 Length = 392 Score = 192 bits (487), Expect = 2e-53 Identities = 142/411 (34%), Positives = 209/411 (50%), Gaps = 44/411 (10%) Query: 71 PSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQ 130 P M R P+ G+ +L+D +G+RYLDA +GIAV GH HP V + + Q RL Sbjct: 4 PLMATYNRLPVTFDRGEGVWLWDTNGKRYLDALSGIAVCGLGHAHPAVRDALCEQAGRLI 63 Query: 131 HPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYT---GCQD--I 185 H + +Y A + AL ++ G + VFF NSG EANE A+ +A+L+ G ++ I Sbjct: 64 HTSNIY-GVAEQERLGALLTEQAG-MDRVFFANSGAEANEAAIKLARLHAHRRGIENPAI 121 Query: 186 VAVRNGYHGNAAATMGATGQSMWKFN---VVQNSVHHALNPDPYRGVFGSDGEKYAKDLQ 242 + + +HG AT+ ATG + +VQ V PY D Sbjct: 122 LVAEHSFHGRTLATLSATGNRKVQAGFEPLVQGFVRV-----PY-------------DDL 163 Query: 243 DLIQYGTTG--HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFAR 300 D I+ T +I + E IQG GGI + YL + ++G L + DE+Q+G R Sbjct: 164 DAIETAATNRPNIVAILIEPIQGEGGIRLPSDDYLVRLREICDRSGWLLMLDEIQTGMGR 223 Query: 301 TGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTA 360 TG + F+ + PD+VT+AKG+GNG P+GA + A V + S+ +TFGGN ++ Sbjct: 224 TGRLFAFQHAGIQPDVVTLAKGLGNGMPIGACLARGAAAEVFSPGSHGSTFGGNPLACRV 283 Query: 361 GLAVLNVIEKEKLQENAAMVGSYLKEKL-TQLKEKHEIIGDVRGRGLMLGVELVSDRKLK 419 G AVL + E L ENAA G+YL + L L E H ++ ++RGRGLM+G+EL DR Sbjct: 284 GRAVLETLIDENLTENAAAQGAYLLDSLRAALGETHGLV-EIRGRGLMVGIEL--DRPCG 340 Query: 420 TPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAM 470 ++ + + G+LI V R+ PPL + D LV + Sbjct: 341 --------ELVGRALDAGLLINVTA--ERVIRLLPPLIIDRAQIDELVATL 381 Lambda K H 0.320 0.136 0.403 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: 429 Number of extensions: 23 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: 477 Length of database: 392 Length adjustment: 32 Effective length of query: 445 Effective length of database: 360 Effective search space: 160200 Effective search space used: 160200 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: 51 (24.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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