Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_012991318.1 THAL_RS01365 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000025605.1:WP_012991318.1 Length = 379 Score = 174 bits (440), Expect = 6e-48 Identities = 128/404 (31%), Positives = 203/404 (50%), Gaps = 47/404 (11%) Query: 74 YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133 Y + P+ V+GK YLYDE G+RYLD +GI + G+ D + AI Q+K L H + + Sbjct: 7 YQRLPVRFVKGKGVYLYDEKGKRYLDLVSGIAVNALGYGDRDQVKAICHQAKKLIHVSNL 66 Query: 134 YLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY-----TGSLEMISLRN 188 + + A+ L + +V +F NSG+EANE A+ + R Y +I+ +N Sbjct: 67 FENPWQEKLAKLLVERFWTKGRV-FFCNSGTEANEAAIKLVRRYFRLRGEDRYRIITFQN 125 Query: 189 AYHGGSSNTIGLTA---LNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIEY 245 ++HG + ++ TA + T PL +G + + N D S K + D Sbjct: 126 SFHGRTFGSMSATAQKKIQTGFEPLLEGFDYAIFN----------DISSVEKLITD---- 171 Query: 246 GTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWG 305 K A + E +QG GG +L+ + ++ R G + + DEVQTG GRTG Y Sbjct: 172 ----KTAAVMLEIVQGEGGVRVADRQFLEDLQKLCRERGLLLLLDEVQTGIGRTGKFY-A 226 Query: 306 FQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVLN 365 +Q + PDI+T+AKG+G G+P+GA++ E+A + +TFGGNP+ A L V+ Sbjct: 227 YQHFQLEPDIITLAKGLGGGVPIGALLAREEVAKAFDAGSHGSTFGGNPLACASALVVVE 286 Query: 366 VIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAET 425 + + +H EVG + ++RL + + G+VRG GLM+ +EL S+ K+ Sbjct: 287 KV--SELLDHVREVGEYFMERLAALGR-----GEVRGMGLMLALELESNCKE-------- 331 Query: 426 SVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDAL 469 V+ + L E G+++ V R PP+ K D V L Sbjct: 332 -VVLKAL-EKGLVINCTA--KKVLRFVPPLILQKRHVDIAVRIL 371 Lambda K H 0.320 0.138 0.412 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: 412 Number of extensions: 25 Number of successful extensions: 5 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: 476 Length of database: 379 Length adjustment: 32 Effective length of query: 444 Effective length of database: 347 Effective search space: 154068 Effective search space used: 154068 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 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