Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_019557719.1 F612_RS0110440 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000381085.1:WP_019557719.1 Length = 392 Score = 172 bits (435), Expect = 2e-47 Identities = 122/409 (29%), Positives = 196/409 (47%), Gaps = 42/409 (10%) Query: 74 YYQKPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTI 133 Y + P+ +G L D G+ YLDA +GI S GH HP I AI +QS+ L H + + Sbjct: 9 YARLPVTFEKGDGATLQDSEGKMYLDAISGIAVTSLGHAHPFISEAICKQSQQLIHTSNL 68 Query: 134 YLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY-----TGSLEMISLRN 188 Y A+ L ++ V+F NSG+EANE A+ +A+ + + ++ + N Sbjct: 69 YHIKKQQMLADQLIEL--SGMEQVFFCNSGAEANEAAIKIAKKFGHQQGITNPTIVVMEN 126 Query: 189 AYHGGSSNTIGLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIE---- 244 ++HG + T+ T NP + G G + + D++ Sbjct: 127 SFHGRTMATLSATG-----------------NPKVHEGFQPLVGG-FTRVPFDNVAAVEA 168 Query: 245 YGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYW 304 + + + E IQG GG GYLK++ +I + + DE+QTG GRTG ++ Sbjct: 169 LSDNRDIVAILVEPIQGEGGVYVPQKGYLKALRKICDANNWLLMIDEIQTGMGRTGQ-WF 227 Query: 305 GFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVL 364 FQ +++ PD++T+AK +GNG+P+GA + + VLA TFGGNP+ A GLAV+ Sbjct: 228 AFQHENITPDVLTLAKALGNGVPIGACIANNKATDVLAPGNHGTTFGGNPLACAVGLAVI 287 Query: 365 NVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAE 424 V+ A+ G+ L+ + K + I +RG+G M+GI+L D+ A+ Sbjct: 288 EVLKTHNYIPAIAKKGALLLNQFKSALTQQPGISSIRGQGYMIGIQL-----DRPCAE-- 340 Query: 425 TSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALDYSI 473 L + E G+L+ G+ R+ P ++ D LV L I Sbjct: 341 ---LVKMALERGLLINV--TRGDTVRLLPSFVMSQQQTDELVTKLSQLI 384 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: 401 Number of extensions: 11 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: 392 Length adjustment: 32 Effective length of query: 444 Effective length of database: 360 Effective search space: 159840 Effective search space used: 159840 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