Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate NP_661271.1 CT0367 acetylornithine aminotransferase
Query= SwissProt::Q940M2 (476 letters) >NCBI__GCF_000006985.1:NP_661271.1 Length = 400 Score = 192 bits (488), Expect = 2e-53 Identities = 124/406 (30%), Positives = 203/406 (50%), Gaps = 37/406 (9%) Query: 72 FHYYQK-PLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHA 130 FH Y + PL+I GK +LY SG RYLD AG+ + G+ + AITEQ+ H Sbjct: 16 FHNYARLPLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLEQAITEQASKYIHV 75 Query: 131 TTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY------TGSLEMI 184 + +++ D A L + V+F NSG+EA E A+ +AR + T +++ Sbjct: 76 SNLFMQKPQFDLAAKLLEI--SRMSKVFFCNSGTEAIEAAIKLARRFAARNGDTDKTQVL 133 Query: 185 SLRNAYHGGSSNTIGLTALNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIE 244 SL N +HG + + LTA + D + + G + DV D +E Sbjct: 134 SLTNCFHGRTYGALSLTAKPKYV--------------DGFEPLVPETGMIDFNDVED-LE 178 Query: 245 YGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYW 304 S + A E +QG GG +++ ++ + E+ + + +ADE+Q G GRTG+ ++ Sbjct: 179 RKVSNRTAAVFVEFVQGEGGIHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGA-FF 237 Query: 305 GFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVL 364 + D+ PD+V +AK +G GLPLGA++ + ++A V TFGGNPV A GLA++ Sbjct: 238 SYMPFDIQPDLVCVAKPLGGGLPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMI 297 Query: 365 NVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAE 424 I + ++ EVGS + + + ++H I ++R GLM+G+ + E Sbjct: 298 EAILADGLMQNALEVGSMMRTAFEKMAEKHAQILEIRQYGLMIGVTV----------HRE 347 Query: 425 TSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALD 470 E+ + G+LV NV R+ PP+ +K++A +D LD Sbjct: 348 AKYYVEEALKRGVLV--NATSNNVIRLLPPLSISKEEAQLCLDTLD 391 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: 421 Number of extensions: 23 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: 400 Length adjustment: 32 Effective length of query: 444 Effective length of database: 368 Effective search space: 163392 Effective search space used: 163392 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