Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_013835847.1 THICY_RS06630 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000214825.1:WP_013835847.1 Length = 390 Score = 177 bits (450), Expect = 4e-49 Identities = 123/407 (30%), Positives = 194/407 (47%), Gaps = 45/407 (11%) Query: 74 YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133 Y + P+ G+ LYDE YLDA +GI S GH HP I A+ EQSK L H + + Sbjct: 8 YGRLPVTFHYGEGALLYDEQDNAYLDAVSGIAVCSLGHAHPAIAQALCEQSKTLIHTSNL 67 Query: 134 Y---LHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGS-----LEMIS 185 Y +GD A++ + V+F NSG+EANE A+ MAR Y S ++I Sbjct: 68 YHVAKQQQLGDKLVAISG-----MDKVFFGNSGAEANEAAIKMARKYGHSKGISHAQIIV 122 Query: 186 LRNAYHGGSSNTIGLTA---LNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDH 242 + N++HG + T+ T ++ YPL +G + P+ V ++ Sbjct: 123 MENSFHGRTLATLSATGSAKVHDGFYPLVEGFVRV-----PFDNVEAVANAI-------- 169 Query: 243 IEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSH 302 + V + E +QG GG PGYLK++ + + + DE+Q G GRTG Sbjct: 170 ---ANNPNVVAILVEPVQGEGGVHVPKPGYLKALRALCDEHDLLLMIDEIQAGIGRTGK- 225 Query: 303 YWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLA 362 ++ FQ + ++PD++++AK +GNG+P+GA + + A + A TFGGNP+ A GLA Sbjct: 226 WFAFQHEGILPDVLSLAKALGNGVPIGASLARGKAAELFAPGNHGTTFGGNPLACAAGLA 285 Query: 363 VLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAK 422 V+ ++ + A+ G+ L+ K + D+RG+G M+GI+L D Sbjct: 286 VIETLEYHNYIDLVAKQGAELLAAFKTALANIPGVVDIRGKGYMIGIQLDRPCGDLVKMA 345 Query: 423 AETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDAL 469 +L R G+ R+ P T ++ LV+ L Sbjct: 346 LADKLLINVTR------------GDTVRLLPTFVMTHAQSEQLVNGL 380 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: 407 Number of extensions: 19 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: 476 Length of database: 390 Length adjustment: 32 Effective length of query: 444 Effective length of database: 358 Effective search space: 158952 Effective search space used: 158952 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