Align branched-chain amino acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate WP_012170125.1 AZC_RS08280 aminotransferase class IV
Query= metacyc::MONOMER-11904 (286 letters) >NCBI__GCF_000010525.1:WP_012170125.1 Length = 261 Score = 139 bits (349), Expect = 9e-38 Identities = 87/243 (35%), Positives = 134/243 (55%), Gaps = 10/243 (4%) Query: 1 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM 60 MK++LNG V+ A+I+ D G GDG+FE I V G +L H+ RL A + + Sbjct: 1 MKLWLNGGLVDAAAARIAPGDRGFTLGDGLFETIAVRGGTPLRLSAHLARLARGAEVIGL 60 Query: 61 DIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPL 120 + T ++S I + N L +A +RL +TRG G G+ P + P+PT+ A PM Sbjct: 61 PLPTF--DLSAIATALLAANGLTDAVLRLTLTRGEGPRGVLPPEAPRPTLLVTAAPMAAP 118 Query: 121 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEGYVAEG 180 + ++ RR L+ +KSLNYL++ILA+ +A AGCD+A LL++ G +AE Sbjct: 119 APPARL-MLAQGTRRNEFSPLS-GIKSLNYLDNILARQEAQRAGCDDALLLNTLGRLAES 176 Query: 181 TGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFI 240 T N+FV ++G++ TPP+S L G+ R V+ +E LT D+ A+E F+ Sbjct: 177 TIANLFVQRDGQLLTPPLSEGALPGVMRAEVL------ARGAVERPLTSDDVATAEEAFL 230 Query: 241 TGT 243 T + Sbjct: 231 TSS 233 Lambda K H 0.319 0.140 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: 159 Number of extensions: 7 Number of successful extensions: 4 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: 286 Length of database: 261 Length adjustment: 25 Effective length of query: 261 Effective length of database: 236 Effective search space: 61596 Effective search space used: 61596 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: 47 (22.7 bits)
This GapMind analysis is from Jul 25 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