Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_072908700.1 BUB13_RS10480 hypothetical protein
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_900142125.1:WP_072908700.1 Length = 291 Score = 215 bits (547), Expect = 1e-60 Identities = 108/275 (39%), Positives = 170/275 (61%), Gaps = 1/275 (0%) Query: 6 IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEI 65 ++LNGEFVP D A++SV+D G LYGDG+FE R +++ +H RL +SA+++ I Sbjct: 4 VYLNGEFVPGDRAQISVFDQGLLYGDGIFESFRSIGDRLYQFDQHYARLLQSAEALNYAI 63 Query: 66 PYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQ 125 PYS E+ +I++E ++N+L N Y R+ ++RG G +G + +V+ + F Sbjct: 64 PYSQQELEDILLELRQRNQLENAYYRITITRGRGEIGFQRNISNDLTCLVMGREFQGFAA 123 Query: 126 EYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAE 185 EYY++GI + TRRN P+ ++P++KS++ LN++L ++EAK AG E +MLN++ ++ E Sbjct: 124 EYYQQGIELRVAQTRRNAPEAINPKIKSISNLNSLLGKLEAKAAGAFEVIMLNNKEHICE 183 Query: 186 GSGDNVFIVKGNKLITPPSSAGALEGITRNAILEI-GEKLGYDVREELFTRHDVYVADEV 244 G+ N+F VK + TP +S G LEG+TR I+ + EKL V F D+ +DEV Sbjct: 184 GASSNIFWVKDKWIFTPDASTGLLEGVTRATIIRLCEEKLNLRVIAGEFKLQDLKFSDEV 243 Query: 245 FLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEE 279 F+T T+ EV+ V VD I GQ G +L +E Sbjct: 244 FITSTSLEVMPVIKVDDFIINQGQVGRIAYQLRKE 278 Lambda K H 0.317 0.138 0.390 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: 217 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: 298 Length of database: 291 Length adjustment: 26 Effective length of query: 272 Effective length of database: 265 Effective search space: 72080 Effective search space used: 72080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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