Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012674308.1 SULAZ_RS02775 aminodeoxychorismate lyase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000021545.1:WP_012674308.1 Length = 249 Score = 89.7 bits (221), Expect = 6e-23 Identities = 70/234 (29%), Positives = 116/234 (49%), Gaps = 11/234 (4%) Query: 28 LYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEIPYSLDEVTNIVVETIRQNKLSN 87 +YG+GVFE R + H RL + A S L P + ++ + + + + + Sbjct: 21 MYGEGVFETFRYKEKLPKYIDYHYKRLIKGA-SFLKIPPITKEDYLYYINQAVNSIEDKD 79 Query: 88 GYIR-LVVSRGAGNLGLDPDSCKKPNVVVIAEQLSLFPQEYYEKGIPVVTVATRRNRPDV 146 YI+ +++S G L P K N++V+ + P + I + + + D Sbjct: 80 LYIKTILLSEGNSYYPLQP---YKSNLLVVVK-----PYKAINTPITLTISPYKVHSKDP 131 Query: 147 LSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAEGSGDNVFIVKGNKLITPPSSA 206 L ++KS NYL NILV+ A+ G +A++LN+ + E S N+F +KG L TP Sbjct: 132 LL-KIKSTNYLRNILVKRYAQEKGFFDAIILNEDDCITETSSANIFWIKGRYLYTPSLEC 190 Query: 207 GALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEVFLTGTAAEVIAVTTVD 260 G LEGI+R ILE G+ G+ V E F D+ A+ +FL+ ++ V ++D Sbjct: 191 GVLEGISRKKILEEGKNQGFVVIEGEFNLKDLKGANLIFLSNALHGIMKVESID 244 Lambda K H 0.317 0.138 0.389 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: 171 Number of extensions: 10 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: 298 Length of database: 249 Length adjustment: 25 Effective length of query: 273 Effective length of database: 224 Effective search space: 61152 Effective search space used: 61152 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: 47 (22.7 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