Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate NP_348843.1 CA_C2226 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000008765.1:NP_348843.1 Length = 280 Score = 96.3 bits (238), Expect = 7e-25 Identities = 77/260 (29%), Positives = 123/260 (47%), Gaps = 24/260 (9%) Query: 3 EQWIFLNGEFVPKDEAKVSVYDHGYLY-GDGVFEGIRVYSGNVFRLREHLVRLYESAKSI 61 E + LN E K +D ++ G ++E IR+ G L H+ RL S K Sbjct: 9 ENYFVLNEEIKDK-----KTFDGNFVENGKSLYEVIRIIDGIPLFLGNHIKRLENSFKIE 63 Query: 62 MLEIPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLS 121 L P SLD I + + I NK G ++LV + C V + Sbjct: 64 KLSFPVSLDNIKQNIFKLIEANKCEVGNVKLV-------FNYFENKCDFYGYFVQHK--- 113 Query: 122 LFPQEY-YEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180 +P EY Y G+ + R+ P+ +V +LN+ N+ +I+ K GV EA++++ Sbjct: 114 -YPDEYDYINGVKTILYHGERSNPNA---KVINLNFRKNVDKKIKEK--GVFEAILVDRN 167 Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 G + EGS N+F+VK N + T P L GITR I+EI ++ GY V +E + Sbjct: 168 GNITEGSKSNIFMVKSNTVYTAPVE-DVLPGITREIIVEICKQCGYTVVDEKINYKKIDQ 226 Query: 241 ADEVFLTGTAAEVIAVTTVD 260 + +F++GT+ +V+ + VD Sbjct: 227 FEGLFISGTSPKVLPICQVD 246 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: 235 Number of extensions: 15 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: 280 Length adjustment: 26 Effective length of query: 272 Effective length of database: 254 Effective search space: 69088 Effective search space used: 69088 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 Apr 10 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