Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_022948766.1 H035_RS0109610 aminodeoxychorismate lyase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000421465.1:WP_022948766.1 Length = 282 Score = 108 bits (271), Expect = 1e-28 Identities = 82/262 (31%), Positives = 127/262 (48%), Gaps = 6/262 (2%) Query: 17 VSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIPLTKEEMIDVVLET 76 V D G YGDG+FE R + GV + H+DRL + L D+P E++ +T Sbjct: 15 VDAADRGFQYGDGLFETFRIHRGVPLFWQRHMDRLRRGCERL--DLPFPSSELLRREADT 72 Query: 77 LRVNNLRDAYIRLVVTRGVGDLGLDPRKCGKPTIFCIAIPMPPLLGEDGIRAITVSV--R 134 + L + ++ +TRG G G P + +PT P+P L E R V + Sbjct: 73 ACMG-LPEGVLKFQLTRGSGGRGYTPPQETQPTRVWRLHPLPDGLEELRKRGARVRLCHT 131 Query: 135 RLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGTGDNIFIVKNGVLK 194 RL ++ +K N L VLA+ + N V E + D +GF+VEGT N+F ++GVL Sbjct: 132 RLGINPALAGIKHCNRLEQVLARKEWNDPSVYEGLMCDGEGFLVEGTLSNVFWRRSGVLI 191 Query: 195 TPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADELFITGTAAEIVPVFE-I 253 TP V + + G+ R V+ A++ V E L A+E+F+T + ++PV + Sbjct: 192 TPRVDRCGVAGVVRAWVLDRARQWNAAVKEVRARPEVLAEAEEVFLTNSVIGVIPVVAGV 251 Query: 254 DGRVINNKQVGEITKKLKEKFK 275 D V + VG T +L +K Sbjct: 252 DRPVRGSWPVGSFTARLMSDWK 273 Lambda K H 0.321 0.143 0.411 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: 205 Number of extensions: 14 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: 288 Length of database: 282 Length adjustment: 26 Effective length of query: 262 Effective length of database: 256 Effective search space: 67072 Effective search space used: 67072 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 09 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