Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate WP_011763948.1 AZO_RS01095 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000061505.1:WP_011763948.1 Length = 460 Score = 167 bits (423), Expect = 7e-46 Identities = 130/406 (32%), Positives = 202/406 (49%), Gaps = 43/406 (10%) Query: 88 YLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALA 147 +L D G+ LDAFAG+ V+ G+ H ++ A EQ + L +AT + + + A LA Sbjct: 40 WLRDIHGKEVLDAFAGLWCVNIGYGHESVVQAAAEQMRKLPYATGYFGFGS--EPAIRLA 97 Query: 148 AKM----PGNLKVVYFVNSGSEANELAMMMARLYTGSL------EMISLRNAYHGGSSNT 197 AK+ P +L+ Y GSEA + A+ + Y + I++ YHG SS Sbjct: 98 AKLAEIAPKSLRHTYLTLGGSEAVDAAIRLITHYYNATGRPQKKHFIAIERGYHGSSSVG 157 Query: 198 IGLTALNTWK--YPLPQGEIHHVVNPDPYRGVFGSD---------GSLYAKDVHDHIEYG 246 GLTAL + + +P H++ +P PYR G D +L AK E G Sbjct: 158 SGLTALPAFHRGFDVPLPNQHYIASPYPYRSPVGDDPQAVIAASVAALRAKVA----ELG 213 Query: 247 TSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGF 306 VA F E +QG GG + G+LK++ E R G + + DEV TGFGRTG + Sbjct: 214 ADN-VAAFFCEPVQGSGGVIVPPKGWLKAMREASRELGILFVVDEVITGFGRTGPMF-AC 271 Query: 307 QTQDVVPDIVTMAKGIGNG-LPLGAVVTTPEIASVLASKILFN-------TFGGNPVCSA 358 +DV PD++TMAKG+ +G +P+GA++ + E+ + +A N T+ G+PV +A Sbjct: 272 LAEDVEPDLMTMAKGLTSGYVPMGALMISDEVYNGIADGAAPNVLVGHGATYSGHPVSAA 331 Query: 359 GGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDK 418 L V+ + ++ H + L ++ H ++GDVR RGL+ +ELV+D+ K Sbjct: 332 VALEVIRLYEEGGILAHAQAMEPGFAAGLGEMLD-HPLVGDVRHRGLLGAVELVADKASK 390 Query: 419 ---TPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDD 461 PA LF + G++ G H + P +CFT+D+ Sbjct: 391 RAFDPALGLADRLFRSGYQNGLIFRSFGDH--ILGFAPALCFTEDN 434 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: 575 Number of extensions: 29 Number of successful extensions: 6 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: 460 Length adjustment: 33 Effective length of query: 443 Effective length of database: 427 Effective search space: 189161 Effective search space used: 189161 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