Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate BPHYT_RS00235 BPHYT_RS00235 4-aminobutyrate aminotransferase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__BFirm:BPHYT_RS00235 Length = 441 Score = 313 bits (801), Expect = 1e-89 Identities = 175/433 (40%), Positives = 257/433 (59%), Gaps = 13/433 (3%) Query: 49 RPYKGPSADE----VLQKRKKFLGPSLFHYYQKPLNIVEGKMQYLYDESGRRYLDAFAGI 104 RP + DE + QKR++ LG S +Y+KP+++V G++QYL+D G +YLD + + Sbjct: 14 RPENAATLDEYTRQLTQKREQLLGGSYRLFYRKPVHLVRGQLQYLWDVHGDKYLDMYNNV 73 Query: 105 VTVSCGHCHPDILNAITEQSKLLQHATTIYLHHAIGDFAEALAAKMPGNLKVVYFVNSGS 164 ++ GHCHP ++ ++ EQ K L + T YLH I + E L MP + ++ +GS Sbjct: 74 ASI--GHCHPAVIASVHEQMKQL-NTHTRYLHERILAYTEELLTTMPSEISRAMYMCTGS 130 Query: 165 EANELAMMMARLYTGSLEMISLRNAYHGGSSNTIGLT-ALNTWKYPLPQGEIHHVVNPDP 223 EAN+LAM +AR Y+G +I R AYHG S T G + AL + + P + + PD Sbjct: 131 EANDLAMRVARAYSGGTGIIVSREAYHGTSYLTSGASPALGSGQPIDPTTRL--IPAPDR 188 Query: 224 YRGVFGSDGSLYAKDVHDHIE-YGTSG-KVAGFIAETIQGVGGAVELAPGYLKSVYEIVR 281 YR G +A ++ I+ G + AGF+A++I G + GYL+ ++V Sbjct: 189 YRVDTPDLGLWFAAEMQKQIDDMAAQGIRFAGFMADSIFSSDGVLPGPAGYLQPAIDVVH 248 Query: 282 NAGGVCIADEVQTGFGRTGSHYWGFQTQDVVPDIVTMAKGIGNGLPLGAVVTTPEIASVL 341 GG+ IADEVQ GF RTG +WGF VVPD+VTM K +GNG+P+ A+ E+ + Sbjct: 249 RNGGIFIADEVQPGFARTGDAFWGFARHGVVPDVVTMGKPMGNGIPVSALFARAEVLAAF 308 Query: 342 ASKI-LFNTFGGNPVCSAGGLAVLNVIDKEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDV 400 + +I FNTFGGNPV A AVLNVI +E+ QEH +VG+ L+ + +RH+ +GDV Sbjct: 309 SDEIPYFNTFGGNPVSMAAAQAVLNVIREERLQEHSQQVGARLLGEFSRLAERHECVGDV 368 Query: 401 RGRGLMVGIELVSDRKDKTPAKAETSVLFEQLRELGILVGKGGLHGNVFRIKPPMCFTKD 460 RG GL +G ELV+DR+ KTP KA + E LR+ +L G HGNV +++PP+ F Sbjct: 369 RGAGLFIGFELVTDRESKTPDKARALDVIENLRDQRVLTSVAGPHGNVLKLRPPLAFQAQ 428 Query: 461 DADFLVDALDYSI 473 D D++V ALD ++ Sbjct: 429 DIDWVVSALDQAL 441 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: 527 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: 441 Length adjustment: 33 Effective length of query: 443 Effective length of database: 408 Effective search space: 180744 Effective search space used: 180744 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