Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_018124587.1 B149_RS0107590 4-amino-4-deoxychorismate lyase
Query= BRENDA::E6TUA8 (302 letters) >NCBI__GCF_000375485.1:WP_018124587.1 Length = 314 Score = 154 bits (389), Expect = 3e-42 Identities = 88/266 (33%), Positives = 142/266 (53%), Gaps = 3/266 (1%) Query: 24 DHGFLYGDGVFEGIRVYDGNIFKLTEHLKRLYESAQSIMLEIPYSKEDFQQIIVDTVRKN 83 DH GDGVFE ++ +G +++L HL+R+ SA++I L P S ++ Q I+D R Sbjct: 49 DHLVHRGDGVFEAMKWVNGKLYQLGAHLERMKRSAKAIHLTPPCSWDELSQTILDVARAA 108 Query: 84 QLESGYIRVVVSRGPGNLGLDPSRCSAPHVIVIAEELALFPKELYELGLTVASVASRRNR 143 + +SG IRV++ RGPG G+DP+ C + V A + P YE G T + + Sbjct: 109 ESDSGMIRVLLGRGPGGFGIDPAECPVASLYVAAFDFQPKPDSFYEKGSTAFKTSVPAKQ 168 Query: 144 PDVLSPQIKSLNYLNNILVKLEANQAGAHEALMLNDQGYVTEGSADNIFIVKNNTIITPP 203 P + + IKS++YL N+L+K EA + G ++ G + EG+ +N+ IV N + P Sbjct: 169 PYLAA--IKSIDYLPNVLMKREAAEKGYDYPFCFDEHGLLAEGATENVCIVDKNGKVHIP 226 Query: 204 VYLGALEGITRNAIIDLAKECGYEMKETPFTRHDVYVADEVFLTGTAAEVIAVVEVDKRM 263 + AL G T ++DL K+ ++ T H++ A EV + GT + I VV + + Sbjct: 227 EFTNALAGTTLMRVVDLIKD-EMDIIFRGITEHEILEAKEVIIVGTTGDAIPVVRFNGKP 285 Query: 264 ISDGKPGKVTNHLLSEFRKVVTTDGI 289 I D +PG V + R+ + +GI Sbjct: 286 IHDVRPGPVAKRIRELIRQDIEANGI 311 Lambda K H 0.318 0.136 0.385 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: 224 Number of extensions: 13 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: 302 Length of database: 314 Length adjustment: 27 Effective length of query: 275 Effective length of database: 287 Effective search space: 78925 Effective search space used: 78925 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 (21.7 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