Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Korea:Ga0059261_4131 Length = 398 Score = 171 bits (434), Expect = 3e-47 Identities = 130/412 (31%), Positives = 194/412 (47%), Gaps = 50/412 (12%) Query: 74 YYQKPLNIVEGKMQYLYD-ESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATT 132 Y + P+ G+ +LY + G YLD AG+ T + GHCHP ++ A+ Q+ L H + Sbjct: 9 YARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISN 68 Query: 133 IYLHHAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGSL------EMISL 186 ++ AE L + V+F NSG+EA E A+ +AR Y + +I Sbjct: 69 MFEMPGQNALAERLTTASFAD--TVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGF 126 Query: 187 RNAYHG---GSSNTIGLTA-LNTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDH 242 A+HG G+ N G A L+ + LP G +H V+ P + +D + Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLP-GFVHFAVDNWPALALAIADSA--------- 176 Query: 243 IEYGTSGKVAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTG-- 300 A + E +QG GGA + +L + G + I DEVQTG GRTG Sbjct: 177 --------TAAVVVEPVQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKL 228 Query: 301 -SHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAG 359 +H W D PDI+ +AK +G+G P+GA + T E AS + + T GGNP+ A Sbjct: 229 FAHQW---YPDATPDIMALAKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAV 285 Query: 360 GLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRH-DIIGDVRGRGLMVGIELVSDRKDK 418 +A + I K + H EV HL L + H +I ++RG+GL+VG+ LV + + Sbjct: 286 AIAAFDEIAKPETLTHAREVAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNR-- 343 Query: 419 TPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKDDADFLVDALD 470 RE +LV GG N R+ PP+ T +AD ++D LD Sbjct: 344 --------AFMAAAREQRLLVAGGG--DNCVRLLPPLTLTVAEADQILDRLD 385 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: 429 Number of extensions: 24 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: 398 Length adjustment: 32 Effective length of query: 444 Effective length of database: 366 Effective search space: 162504 Effective search space used: 162504 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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