Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012474057.1 CPHAMN1_RS03045 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000020545.1:WP_012474057.1 Length = 303 Score = 332 bits (852), Expect = 5e-96 Identities = 162/301 (53%), Positives = 215/301 (71%), Gaps = 4/301 (1%) Query: 5 KADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDS 64 K++ IW NGE+V W DAK+H++SH +HYG+S FEGIRCY++ KGP + EH++RL+DS Sbjct: 3 KSEKIWMNGELVDWNDAKIHILSHVIHYGSSTFEGIRCYETTKGPAILFLDEHIRRLYDS 62 Query: 65 AKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAA 124 +KIYR + S+ E+ A D I+ N S YIRPL++ G +GVNP + +V IA Sbjct: 63 SKIYRIEIPYSMAEIRTAVIDTIKANGHKSCYIRPLVYRGQGALGVNPHLA-AIEVAIAT 121 Query: 125 FPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGI 184 + WG YLG + LE G+D VSSWNR APNT+PT AKAGGNYL+S L+ EA Y EGI Sbjct: 122 WEWGTYLGEDVLETGVDVRVSSWNRLAPNTLPTWAKAGGNYLNSQLIKMEAIMDNYAEGI 181 Query: 185 ALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSR 244 LD+NGY+SEG+GEN+F ++DG+++TP S L G+TR AII +AKELG EVRE ++ R Sbjct: 182 GLDINGYVSEGSGENIFIIRDGIIYTPMTGQSVLAGLTRQAIIHIAKELGYEVRETMIPR 241 Query: 245 ESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLF-TGETEDKWGW 303 E+LY+ADEVF++GTAAEITPVRS+D VG GPVT+ +Q + + TG ED + W Sbjct: 242 EALYIADEVFLTGTAAEITPVRSIDKHPVGNEIRGPVTEILQSHYLKIIQTG--EDPYNW 299 Query: 304 L 304 L Sbjct: 300 L 300 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: 313 Number of extensions: 5 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: 309 Length of database: 303 Length adjustment: 27 Effective length of query: 282 Effective length of database: 276 Effective search space: 77832 Effective search space used: 77832 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 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