Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__BFirm:BPHYT_RS10155 Length = 433 Score = 210 bits (534), Expect = 9e-59 Identities = 137/410 (33%), Positives = 217/410 (52%), Gaps = 14/410 (3%) Query: 77 KPLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHATTIYLH 136 +P+ I + ++YD GR LD +G ++ GH HP+I++ I E + L H + L Sbjct: 25 EPMIIERAQGSFVYDADGRAILDFTSGQMSAVLGHSHPEIVSVINEYAGKLDHLFSGMLS 84 Query: 137 HAIGDFAEALAAKMPGNLKVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSSN 196 + D A LA P L +++G+E+NE A+ MA+L TG E++ ++HG ++ Sbjct: 85 RPVVDLATRLAEITPDGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTAA 144 Query: 197 TIGLTALNTWKYPLPQGEIHHVVNPDP--YRGVFGSDGSL-YAKDV---HDHIEYGTSGK 250 T + + + + P P YR F G Y ++ D I+ +SG Sbjct: 145 AASAT-YSAGRKGVGPAAVGSFAIPAPFLYRPRFERHGDYDYLAELDYAFDLIDRQSSGN 203 Query: 251 VAGFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQD 310 +A FIAE I GG +EL GY+ ++ G + I DE QTG GRTG+ + Q Sbjct: 204 LAAFIAEPILSSGGIIELPEGYMTALKRKCEERGMLLILDEAQTGVGRTGTMF-ACQRDG 262 Query: 311 VVPDIVTMAKGIGNGLPLGAVVTTPEIASVL--ASKILFNTFGGNPVCSAGGLAVLNVID 368 V PDI+T++K +G GLPL AVVT+ +I + + T +P+ +A GL VL V++ Sbjct: 263 VTPDILTLSKTLGAGLPLAAVVTSAQIEERAHELGYLFYTTHVSDPLPAAVGLRVLEVVE 322 Query: 369 KEKRQEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVL 428 ++ +G+ L + L D+ +R D IGD+RGRGL++G+E+V DR+ K PA + + Sbjct: 323 RDGLVARANLMGARLKRGLLDLMERFDCIGDIRGRGLLLGMEIVKDRRTKEPADGLGAKI 382 Query: 429 FEQLRELGI---LVGKGGLHGNVFRIKPPMCFTKDDADFLVDALDYSISR 475 + LG+ +V G+ G VFRI PP+ +D+ D +D L +I R Sbjct: 383 TRECMNLGLSMNIVQLPGM-GGVFRIAPPLTVHEDEIDLGLDLLGQAIER 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: 446 Number of extensions: 18 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: 433 Length adjustment: 33 Effective length of query: 443 Effective length of database: 400 Effective search space: 177200 Effective search space used: 177200 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