Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_017549174.1 C792_RS0109150 D-amino-acid transaminase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000330705.1:WP_017549174.1 Length = 282 Score = 154 bits (390), Expect = 2e-42 Identities = 98/277 (35%), Positives = 151/277 (54%), Gaps = 9/277 (3%) Query: 1 MKI-YLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLC 59 MKI + NG+F ++++ +V D +GDGV+E IR YDG F LK H+DRL +S + Sbjct: 1 MKISFYNGEFKEDEELRVMYQDRAFYFGDGVYEVIRYYDGEFFTLKGHLDRLMNSMSEIE 60 Query: 60 IDIPLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGLDPRKCGKPTIFCIA--IPM 117 ID + + E++D+V E N + + + + V+RG+ + KP + Sbjct: 61 ID-GVERTELLDIVTELKERNTIENGALYIQVSRGIQNRNHAYPVDVKPVVLAYINEARR 119 Query: 118 PPLLGEDGIRAITVSVRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFV 177 P E G+ IT R L VKSLN L +V+ K +A AG E + D G V Sbjct: 120 PHSQSEHGVHVITNEDYRW----LKCHVKSLNLLANVMEKERAVKAGAHETVMHRD-GVV 174 Query: 178 VEGTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADE 237 EG+ N+FIV+NG+LKT P IL GITR V+++A E + V E ++ ++ A+E Sbjct: 175 TEGSSTNVFIVRNGILKTHPADNLILNGITRQEVLRIAGELDVPVEEAGFSVEEMMDAEE 234 Query: 238 LFITGTAAEIVPVFEIDGRVINNKQVGEITKKLKEKF 274 + IT T E+ PV ++D +I N Q G +T++++ F Sbjct: 235 VIITSTTQEVTPVVKVDDTIIGNGQRGMVTRRIQRVF 271 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: 243 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: 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 Jul 26 2024. The underlying query database was built on Jul 25 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