Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__ANA3:7023380 Length = 405 Score = 172 bits (435), Expect = 2e-47 Identities = 115/342 (33%), Positives = 175/342 (51%), Gaps = 36/342 (10%) Query: 82 VEGKMQYLYDESGRRYLDAFAGIVTVSC-GHCHPDILNAITEQSKLLQHATTIYLHHAIG 140 V G+ ++D+ G ++D FAG + V+C GHCHP ++NA+ Q + L H + + + Sbjct: 28 VRGEGSRVWDQEGNEFID-FAGGIAVNCLGHCHPALVNALKTQGEKLWHLSNVMTNEP-- 84 Query: 141 DFAEALAAKMPGNL--KVVYFVNSGSEANELAMMMARLYTGSL------EMISLRNAYHG 192 A LA K+ + + VYF NSG+EANE A+ +AR Y E+I+ A+HG Sbjct: 85 --ALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKFGVEKDEIIAFDKAFHG 142 Query: 193 GSSNTI---GLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIEYGTSG 249 + T+ G A + P PQ H PY V +E S Sbjct: 143 RTFFTVSVGGQAAYSDGFGPKPQSITHL-----PYNDVAA-------------LEAAVSD 184 Query: 250 KVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQ 309 K + E +QG GG ++ P +LK+V E+ + I DEVQTG GRTG Y + Sbjct: 185 KTCAIMLEPLQGEGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELY-AYMGT 243 Query: 310 DVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVLNVIDK 369 D+VPDI+T AK +G G P+ A++TT EIA L +T+GGNP+ A G AVL+V++ Sbjct: 244 DIVPDILTTAKALGGGFPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNT 303 Query: 370 EKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIEL 411 + L L + +++ + ++RG+GL++G L Sbjct: 304 PEVLNGVKHREQLLRDGLNKINEKYHVFSEIRGKGLLLGAVL 345 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: 437 Number of extensions: 21 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: 405 Length adjustment: 32 Effective length of query: 444 Effective length of database: 373 Effective search space: 165612 Effective search space used: 165612 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 09 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