Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_019865474.1 METMI_RS0106555 D-amino acid aminotransferase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000384075.1:WP_019865474.1 Length = 280 Score = 155 bits (392), Expect = 1e-42 Identities = 105/287 (36%), Positives = 155/287 (54%), Gaps = 15/287 (5%) Query: 1 MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60 M + ++LNG ++P +EAKVSV D G+L+GDG++E I Y G +FRL +HL RL S Sbjct: 1 MASKTVYLNGHYLPLEEAKVSVLDRGFLFGDGIYEVIPAYHGKLFRLDDHLQRLENSLAI 60 Query: 61 IMLEIPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLG--LDPDSCTKPNVVVIAE 118 + + P+S E I + +K N YI L ++RG P+ P V V+ Sbjct: 61 VRITNPHSRSEWQAIFAPLLDADK--NQYIYLQITRGPAEKRDHAFPEGVA-PTVFVMCS 117 Query: 119 QLSLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLN 178 ++ F + GI VT+ R + K++ L NIL R EA G EA+++ Sbjct: 118 DIAPFAGA--QTGIKAVTLDDSRWK----LCHAKTITLLANILHRQEAIDQGGAEAILIK 171 Query: 179 DQGYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDV 238 D GYV EG+ NVF V L+TPP S G L GITR+ ILE+ K RE L ++ Sbjct: 172 D-GYVTEGAASNVFAVINGVLVTPPKSNGILPGITRDVILELAGKNNIAWREGLIALDEL 230 Query: 239 YVADEVFLTGTAAEVIAVTTVDGRTIGLGQTGP--HT-NRLLEEFRK 282 A E+++T + E++AV +DG +G G GP HT N +L+ +++ Sbjct: 231 KSASEIWVTSSTREIVAVIELDGAVVGNGTLGPVWHTMNDILQAYKE 277 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: 201 Number of extensions: 10 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: 298 Length of database: 280 Length adjustment: 26 Effective length of query: 272 Effective length of database: 254 Effective search space: 69088 Effective search space used: 69088 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