Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012567072.1 RC1_RS09070 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000016185.1:WP_012567072.1 Length = 299 Score = 200 bits (509), Expect = 3e-56 Identities = 112/291 (38%), Positives = 161/291 (55%), Gaps = 9/291 (3%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IWF+GEMV W DAK+HV++H LHY + VFEG R Y+ VF+ EH +RL S +I Sbjct: 13 IWFDGEMVPWRDAKIHVLTHGLHYASCVFEGERVYNGK----VFKLTEHSERLVRSGEIL 68 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 F + S E+ +A DV++ + + Y+RP+ + G MGV+ A + IAA+ W Sbjct: 69 GFRIPYSAAEIEKATNDVVKAAGMVNGYVRPVAWRGSEMMGVSAQAN-KIHLAIAAWEWP 127 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 +Y E +GI +S W R AP+T PTA+KA G Y+ + A G+Q+ + LD Sbjct: 128 SYFSPELRMKGISLQISKWRRPAPDTAPTASKAAGLYMICTMSKHAAENDGFQDALMLDY 187 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 G ++E G N+F VKDG + TP L GITR +I LA+ G +V E+ +S + L Sbjct: 188 RGLVAEATGANIFLVKDGAIHTPT-PDCFLDGITRRTVIGLARRRGYQVVERAISADELK 246 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETED 299 EVF++GTAAE+T V + I G +TK + + L G D Sbjct: 247 DFTEVFLTGTAAEVTAVGRIGDITYTPGE---ITKALMLDYDALVNGRLAD 294 Lambda K H 0.319 0.136 0.413 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: 250 Number of extensions: 17 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: 309 Length of database: 299 Length adjustment: 27 Effective length of query: 282 Effective length of database: 272 Effective search space: 76704 Effective search space used: 76704 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: 48 (23.1 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