Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_006748605.1 THITH_RS06115 cytochrome c550
Query= curated2:O29329 (290 letters) >NCBI__GCF_000227685.2:WP_006748605.1 Length = 289 Score = 142 bits (359), Expect = 7e-39 Identities = 90/278 (32%), Positives = 150/278 (53%), Gaps = 8/278 (2%) Query: 2 LYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDL 61 + +++G++ P +S D GFL+GDGV+E I +Y G +F H++RL S A+ + Sbjct: 1 MIAFLNGDYRPLESVCISPLDRGFLFGDGVYEVIPSYRGVLFEADAHLERLRRSLAAVRI 60 Query: 62 EIPITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKL 121 P+ + ++ L N D I VTRG+ + ++ + P Sbjct: 61 ADPLEGAAWRAMLERLLSLNPGGDRAIYLQVTRGVAAREHAFPETAAATVFAMVNPIRSP 120 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 +L E+G+ AIT+ +R +IK++ L N+LA+ +A +G EAI L RNG V Sbjct: 121 EPELAERGVAAITLPDQRWG----RCDIKAVTLLPNVLARQQAAEQGAVEAILL-RNGQV 175 Query: 182 SEGSGDNIFVVKNGAITTPPTINN--LRGITREAVIEIINRLGIPFKETNIGLYDLYTAD 239 +EG+ N+FVV++G + TPP +N+ L GITR +I+++ E IG L AD Sbjct: 176 TEGAASNVFVVRDGRVQTPP-LNDAILPGITRRVLIDVLRDTARACVEQPIGEDQLRAAD 234 Query: 240 EVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEF 277 E+++T + E+ P+ +DGR +GDG PG + R+ + + Sbjct: 235 EIWLTSSTKELLPVTRLDGRAVGDGCPGPVWREALAAY 272 Lambda K H 0.319 0.142 0.409 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: 230 Number of extensions: 12 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: 290 Length of database: 289 Length adjustment: 26 Effective length of query: 264 Effective length of database: 263 Effective search space: 69432 Effective search space used: 69432 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 (21.7 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