Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate CCNA_01818 CCNA_01818 D-alanine aminotransferase
Query= curated2:O29329 (290 letters) >FitnessBrowser__Caulo:CCNA_01818 Length = 287 Score = 139 bits (351), Expect = 6e-38 Identities = 86/274 (31%), Positives = 145/274 (52%), Gaps = 6/274 (2%) Query: 3 YVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLE 62 + Y++G FV EA V I D G+ DGV+E ++G++ + H RL+ S + + Sbjct: 4 FAYVNGRFVRHGEAAVHIEDRGYQLADGVYEVWAVFDGKLADAEGHFARLWRSLDELRIA 63 Query: 63 IPITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLG-LDPRKCQNPSIIVITKPWGKL 121 P+++ ++ E +R+N +R+ VTRG+ P PS++V + + Sbjct: 64 HPMSEAALTMVLREAVRRNKVREGLCYLQVTRGVARRDHAFPNPAVLPSVVVTARSLDRA 123 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 + + A ++V+ N + +IKS+ L N LAK A +G EA F+D G V Sbjct: 124 ASEA-KAAQGASVISVQENRWGRC--DIKSIGLLPNALAKQAARERGAIEAWFVDDMGLV 180 Query: 182 SEGSGDNIFVVK-NGAITTPPT-INNLRGITREAVIEIINRLGIPFKETNIGLYDLYTAD 239 +EG+ N ++V GA+ T T N LRG+TR ++++I G+ E + + +A Sbjct: 181 TEGASSNAWIVDAEGALRTRDTNANILRGVTRYTLLDVIRESGMVINEKPFTIAEAQSAR 240 Query: 240 EVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKL 273 E F+TG + + PIV +DG K+GDGKPG + ++L Sbjct: 241 EAFITGAGSLVTPIVQVDGVKLGDGKPGPVAKRL 274 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: 201 Number of extensions: 9 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: 287 Length adjustment: 26 Effective length of query: 264 Effective length of database: 261 Effective search space: 68904 Effective search space used: 68904 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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