Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_050655903.1 C1M55_RS30495 alpha-ketoacid dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_002893965.1:WP_050655903.1 Length = 334 Score = 447 bits (1150), Expect = e-130 Identities = 215/327 (65%), Positives = 261/327 (79%), Gaps = 1/327 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M +TMA+ALNTALRD+L D ++FGED+G LGGVFR+TDGL +FGD+RCFDTPLAE Sbjct: 1 MPMLTMAQALNTALRDSLAADDNVVVFGEDVGTLGGVFRVTDGLTRDFGDDRCFDTPLAE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 S I+G A+GMAM G+RPVVEMQFDAFAYPAFEQ+ SHVAK+RNRT+GA+ +P+ IR+P+ Sbjct: 61 SGIIGFAIGMAMAGFRPVVEMQFDAFAYPAFEQIASHVAKIRNRTKGALSIPIVIRVPFA 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 GGIGGVEHH DSSE YY TPGL VV P+T DAYSLLR +I DPV+FLEPK+LY+ + Sbjct: 121 GGIGGVEHHCDSSEGYYAHTPGLKVVAPSTVEDAYSLLRSAIEDLDPVIFLEPKKLYFAR 180 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMP 240 + L P+G AV+RR G ATLIAYGP+V AL +AEAAA G D+EVID+R+++P Sbjct: 181 ADVELTA-CEPIGRAVVRRPGRDATLIAYGPSVDVALRSAEAAAAEGRDIEVIDIRSIVP 239 Query: 241 LDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYPP 300 DD TV ASVR+TGR +V+ EA GFAG GAEIAAR+ ERCF+HL APV RV+GFD+PYP Sbjct: 240 FDDETVTASVRKTGRCIVIQEAQGFAGVGAEIAARVQERCFHHLHAPVLRVSGFDIPYPA 299 Query: 301 PLLERHYLPGVDRILDAVASLEWEAVP 327 P LERH+LP VDR+LDAV L+W P Sbjct: 300 PKLERHHLPSVDRVLDAVDRLQWNDAP 326 Lambda K H 0.322 0.138 0.418 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: 386 Number of extensions: 13 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: 328 Length of database: 334 Length adjustment: 28 Effective length of query: 300 Effective length of database: 306 Effective search space: 91800 Effective search space used: 91800 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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