Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate BWI76_RS14455 BWI76_RS14455 aspartate aminotransferase family protein
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__Koxy:BWI76_RS14455 Length = 447 Score = 199 bits (505), Expect = 2e-55 Identities = 152/429 (35%), Positives = 218/429 (50%), Gaps = 37/429 (8%) Query: 78 PLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHA-TTIYLH 136 P V + Y+ D SG+RYLDA G GH HPD+L A+ Q L +A T+ + Sbjct: 13 PAVAVSAQGAYITDASGQRYLDACGGAAVSCLGHAHPDVLAAMHRQIDRLAYAHTSFFTS 72 Query: 137 HAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGSLEM------ISLRNAY 190 + AE L PG+L YFV+ GSEA E A+ +AR Y + I+ + +Y Sbjct: 73 DTVEQLAEQLVRTAPGSLNYAYFVSGGSEAVETALKLARQYFVEIGQPDRTLFIARKQSY 132 Query: 191 HGGSSNTIGLTAL--NTWKY----PLPQGEIHHVVNPDPYRG-VFGSDGSLYAKDVHDHI 243 HG NT+G A+ N W+ PL ++ V + YR G Y + + + Sbjct: 133 HG---NTLGALAVGGNEWRRRQFAPLLM-DVVRVSACNEYRDREAGESQQQYTERLLGEL 188 Query: 244 EYGTSG----KVAGFIAETIQGVG-GAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGR 298 E K+ GFIAET+ G GA+ PGYL+ V + G + IADEV G GR Sbjct: 189 EAAILDAGPEKIIGFIAETVVGATTGAMPPTPGYLQGVRRLCDKYGILYIADEVMCGMGR 248 Query: 299 TGSHYWGFQTQDVVPDIVTMAKGIGNGL-PLGAVVTTPEIASVL-ASKILF---NTFGGN 353 TG+ + F+ VVPDIVT+AKG+G G P+GAV+ + +I + L A +F +T+ + Sbjct: 249 TGTLH-AFEQDGVVPDIVTIAKGLGGGYQPIGAVLASEQIVAALQAGSGMFQHGHTYICH 307 Query: 354 PVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVS 413 P +A LAV VI++++ E + G++L Q L DV +GD RGRGL G+ELV Sbjct: 308 PTAAAAALAVQQVIERDRLLEQVQQQGAYLQQALHDVLGGLPYVGDTRGRGLFAGVELVC 367 Query: 414 DRKDKT---PAKAETSVLFEQLRELGILVGK-----GGLHGNVFRIKPPMCFTKDDADFL 465 D++ KT P + + Q G+LV G G+ I PP ++ + DF+ Sbjct: 368 DKERKTAFDPLLKLHAAIKAQCMGHGLLVYPMGGTIDGQRGDHILIAPPFIVSRSELDFV 427 Query: 466 VDALDYSIS 474 VD L IS Sbjct: 428 VDTLHKVIS 436 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: 516 Number of extensions: 28 Number of successful extensions: 7 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