Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_106716646.1 CU100_RS11145 D-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_003010935.1:WP_106716646.1 Length = 288 Score = 150 bits (380), Expect = 3e-41 Identities = 92/280 (32%), Positives = 148/280 (52%), Gaps = 13/280 (4%) Query: 7 FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66 ++NG++V EA + + D GY + DGV+E + GN+ + HL RL S + + P Sbjct: 6 YVNGQYVQHSEAAIHIEDRGYQFADGVYEVCEIARGNIMDMTRHLDRLDRSLAELKIAWP 65 Query: 67 YSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLG-LDPDSCTKPNVVVIAEQLSLFPQ 125 + ++ E +R NK+ NG + + V+RG + P+ T P +V+ A++ S PQ Sbjct: 66 MGRSALQIVIKEVVRLNKVHNGLVYMQVTRGVARRDHVFPEVDTPPAIVITAKRTS--PQ 123 Query: 126 ---EYYEKGIPVVTVATRR-NRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQG 181 KGI V+TV R +R D +KS+ L N+L R +A+ G QEA ++ G Sbjct: 124 ASAARAAKGIKVITVPENRWDRVD-----IKSIGLLPNVLARQQAREEGAQEAWFVDPDG 178 Query: 182 YVAEGSGDNVFIV-KGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 V EG+ N +IV + L+T P+ +G L GITR I ++ +KLG + E F+ + Sbjct: 179 TVKEGAATNAWIVTRDGVLVTRPAESGILRGITRTTIFDVAKKLGLRIEERGFSVDEAKK 238 Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEF 280 + EVF+T + V+ + +DG ++ G G T L E F Sbjct: 239 SKEVFMTAASTVVMPIVAIDGESVANGHPGTTTLSLREAF 278 Lambda K H 0.317 0.138 0.390 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: 213 Number of extensions: 12 Number of successful extensions: 3 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: 298 Length of database: 288 Length adjustment: 26 Effective length of query: 272 Effective length of database: 262 Effective search space: 71264 Effective search space used: 71264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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