Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate GFF2997 PGA1_c30460 D-alanine aminotransferase Dat
Query= curated2:Q58414 (288 letters) >FitnessBrowser__Phaeo:GFF2997 Length = 286 Score = 150 bits (380), Expect = 2e-41 Identities = 91/272 (33%), Positives = 146/272 (53%), Gaps = 3/272 (1%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 +Y+NG ++ E DAK+S+FD G L DGV+E G + + H RL S L + Sbjct: 5 VYVNGDYLPEGDAKISIFDRGFLMADGVYEVTSVLGGKLIDFEGHAVRLKRSLDELEMAE 64 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGV-GDLG-LDPRKCGKPTIFCIAIPMPPL 120 P +KEE++++ + + +N + + + L VTRG GD + P KPTI P L Sbjct: 65 PCSKEELLEIHRKLVALNEIEEGLVYLQVTRGSDGDRDFVFPSADTKPTIVLFTQNKPGL 124 Query: 121 LGEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEG 180 + + + +K++ L + K+ A AG D+A++++D G V EG Sbjct: 125 ADSPAAKKGAKIISIEDIRWGRRDIKTVQLLYPSMGKMMAKKAGADDAWMIED-GHVTEG 183 Query: 181 TGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFI 240 T +N + VKNGV+ T P+ IL GITR V+++A+E +++ E T+ + ADE F Sbjct: 184 TSNNAYFVKNGVIVTRPLSNDILHGITRKAVLRMAEEAQMKIEERLFTIEEAKEADEAFT 243 Query: 241 TGTAAEIVPVFEIDGRVINNKQVGEITKKLKE 272 T +A ++PV EIDG + + G I K+L+E Sbjct: 244 TSASAFVMPVVEIDGVALGDGTPGPIAKRLRE 275 Lambda K H 0.321 0.143 0.411 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: 241 Number of extensions: 13 Number of successful extensions: 2 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: 288 Length of database: 286 Length adjustment: 26 Effective length of query: 262 Effective length of database: 260 Effective search space: 68120 Effective search space used: 68120 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: 47 (22.7 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