Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_083789992.1 TCUR_RS10125 4-amino-4-deoxychorismate lyase
Query= BRENDA::F2L0W0 (295 letters) >NCBI__GCF_000024385.1:WP_083789992.1 Length = 251 Score = 111 bits (278), Expect = 1e-29 Identities = 93/256 (36%), Positives = 127/256 (49%), Gaps = 24/256 (9%) Query: 27 GFGVFEGIRAYWNGENLYVFRLRDHMERLLRSAKIIGLDVPYTAEELSKAVVETVRANGF 86 G GVFE ++A +GE F L H+ RL RSA +GL P AE L V E + A Sbjct: 4 GDGVFETVKAV-HGEP---FALSRHLRRLARSAAGLGLPEP-DAEALRAGVAEVLAAAPD 58 Query: 87 KEDLYIRPVAYISKPQISLDVRGLQASVA--IAAI--PFGKYLKVEGVRAAVVSWRRVHT 142 IR + Y S P RG + + A IAA PF KV VV WRR Sbjct: 59 WPLARIR-ITYTSGPGPLGSDRGAEGTTATIIAAEQKPFPPTAKV-----CVVPWRRNEH 112 Query: 143 SMMPVMAKATGIYLNSIMAAVEARARGYDEAIMLNAEGKVVEGSGENIFIVRRGVLMTPP 202 + + + Y ++++A A+ RG EAI N G + EG+G N+F+VR G L+TPP Sbjct: 113 GALAGLKTVS--YADNVIALAYAKKRGGGEAIFGNLAGDLCEGTGSNVFVVRDGRLITPP 170 Query: 203 LEDGILEGITRETVISIAGDLGIPLLEKSITREELYAADEAFFVGTAAEITPIIEIDGRV 262 L G L G+TRE V+ G E+++ E + EAF T ++ PI ID V Sbjct: 171 LSSGCLAGVTRELVLEWCGG-----EEENLPLSEFTSVSEAFLTSTTRDVQPIAAIDDVV 225 Query: 263 LQR--GPITQKIAETY 276 L GP+T K+ +T+ Sbjct: 226 LPAAPGPVTAKVMQTF 241 Lambda K H 0.320 0.138 0.396 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: 162 Number of extensions: 6 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: 295 Length of database: 251 Length adjustment: 25 Effective length of query: 270 Effective length of database: 226 Effective search space: 61020 Effective search space used: 61020 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 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