Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 176 bits (446), Expect = 1e-48 Identities = 142/419 (33%), Positives = 202/419 (48%), Gaps = 35/419 (8%) Query: 82 VEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHA-TTIYLHHAIG 140 V G + D +G RY+DA G GH HP ++ AI Q + L +A T+ + Sbjct: 17 VRGDGIEIVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSFFTTEPAE 76 Query: 141 DFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLY---TGSLE---MISLRNAYHGGS 194 A+ L P NL VYFV+ GSEA E A+ +AR Y G E I+ R +YHG Sbjct: 77 ALADLLIEAAPRNLGHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIARRQSYHG-- 134 Query: 195 SNTIGLTAL--NTWKYP--LP-QGEIHHVVNPDPYRGV-FGSDGSLYAKDVHDHIEYGT- 247 NT+G A+ N W+ LP E HHV YR G +A+ + D +E Sbjct: 135 -NTLGALAIGGNAWRREPFLPILIEAHHVTPCFAYREQQAGETDEAFAQRLADELEAKIL 193 Query: 248 ---SGKVAGFIAETIQGV-GGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHY 303 + VA F+AET+ G GAV Y + + + G + I DEV +G GRTG H Sbjct: 194 ELGAQSVAAFVAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGMGRTG-HL 252 Query: 304 WGFQTQDVVPDIVTMAKGIGNGL-PLGAVVTTPEIASVLASKILF----NTFGGNPVCSA 358 + + V PDI+ +AKG+G G P+GA + + EI + + F +T+ G+ A Sbjct: 253 FACEEDGVSPDILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTYIGHATACA 312 Query: 359 GGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDK 418 L V VI +E+ ++ G L RL++ Q H IGDVRGRGL G+ELV DR K Sbjct: 313 AALEVQKVIAEEQLLDNVKARGEQLRARLREWQANHPFIGDVRGRGLFTGVELVQDRASK 372 Query: 419 T---PAKAETSVLFEQLRELGILV-----GKGGLHGNVFRIKPPMCFTKDDADFLVDAL 469 T P +++ + + G++V G G+ I PP T D +V+ L Sbjct: 373 TAFDPKHKLHAIIKSEAMKRGLMVYPMGGTVDGRIGDHVLIAPPFITTSAQIDTIVERL 431 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: 515 Number of extensions: 25 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: 447 Length adjustment: 33 Effective length of query: 443 Effective length of database: 414 Effective search space: 183402 Effective search space used: 183402 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