Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 196 bits (499), Expect = 1e-54 Identities = 139/434 (32%), Positives = 212/434 (48%), Gaps = 19/434 (4%) Query: 59 DVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDV 118 D L+++ EF S + PL I + +L D ++YLD AG + GH HPDV Sbjct: 21 DTFLARQAEFESNVRSYPRKLPLAITKAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDV 80 Query: 119 VEPVINQIKRLQHPTVLYLNHAIAD-FSEALASKLPGDLK---VVFFTNSGTEANELALM 174 ++ + + I L L + D FSE L S LPG+ K + F SG +A E AL Sbjct: 81 LQSIQSVITSGLPLHTLDLTTPLKDRFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALK 140 Query: 175 MAKLYTGCQDIVAVRNGYHGNAAATMGATGQSMWK--FNVVQNSVHHALNPDPYRGVFGS 232 +AK YTG +++ GYHG + TG K N + V P YR G Sbjct: 141 LAKKYTGRSSVISFSGGYHGMTHGALSVTGNLSPKAAVNGMMPEVQFMPYPHQYRCPLGI 200 Query: 233 DGEKYAKDL----QDLIQYGTTG--HIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAG 286 GE K L ++LI +G A I EA+QG GG+ +L ++ G Sbjct: 201 GGEAGVKALTYYFENLINDVESGVRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHG 260 Query: 287 GLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRS 346 L I DEVQ+GFARTG F+ FE + PDI+ M+K +G G PL AV+ + Sbjct: 261 ILLIIDEVQAGFARTGKFFAFEHAGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGH 319 Query: 347 YFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGL 406 + TF GN ++ GL L ++ K+ + A G +LK KL ++++++ +IG VRG GL Sbjct: 320 HTGTFRGNQLAMATGLTTLRHLKDNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGL 379 Query: 407 MLGVELVSDRKLKT-----PATAETLHIMD-QMKELGVLIGKGGYFGNVFRITPPLCFTK 460 M+G+E+V + PA E ++ + E G+++ +GG G V R+ P L + Sbjct: 380 MIGIEIVKPNEAPDHMGCYPADGELSALLQKKCFEAGLILERGGRHGCVLRLLPSLLISN 439 Query: 461 DDADFLVEAMDYSM 474 + + + + ++ Sbjct: 440 AELEIFFDKFEQAL 453 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: 520 Number of extensions: 33 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: 461 Length adjustment: 33 Effective length of query: 444 Effective length of database: 428 Effective search space: 190032 Effective search space used: 190032 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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