Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AZOBR_RS26490 AZOBR_RS26490 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__azobra:AZOBR_RS26490 Length = 324 Score = 233 bits (593), Expect = 6e-66 Identities = 140/319 (43%), Positives = 183/319 (57%), Gaps = 14/319 (4%) Query: 9 ALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAILGTAV 68 A+ AL DA+ DP +L GED+ A GG F+ T GL G ER DTP++E++++G AV Sbjct: 10 AVAQALNDAMAADPAVMLMGEDVAAAGGPFKATRGLLDAHGPERVRDTPISEASLVGAAV 69 Query: 69 GMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGIGGVEH 128 G A+ G +PVVE+ F F A + +V+ AK R G +P+ +R P+GGG+ Sbjct: 70 GAALTGMKPVVEIMFMDFVTLAMDAVVNQAAKARFMFGGQCSVPMVLRTPHGGGLNAGPQ 129 Query: 129 HSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKEALGLPVD 188 HS E ++ PGL VV PAT ADAYSLLR +I +PDPVV +E K LY AL +D Sbjct: 130 HSQCLEAWFAHIPGLRVVCPATVADAYSLLRAAIEAPDPVVVVENKALY----ALQGDID 185 Query: 189 TG---PLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLMPLDDAT 245 +G A I R G AT++ YG + A AA+ A G + E++DLR + P D+ Sbjct: 186 VNAPREVGKARIDRAGRDATIVTYGATLYAARAAADRLATEGIEAEIVDLRWIQPWDEEA 245 Query: 246 VCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYPP----P 301 V ASV +T R V+ HEA G GAEIAARI F L+APV RV P+ P Sbjct: 246 VFASVAKTHRVVIAHEAVQAFGVGAEIAARIAADAFDDLDAPVLRV---GAPFMPIAFAK 302 Query: 302 LLERHYLPGVDRILDAVAS 320 LE YLP DRI+ AV S Sbjct: 303 TLEAAYLPDADRIVAAVKS 321 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: 282 Number of extensions: 9 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: 328 Length of database: 324 Length adjustment: 28 Effective length of query: 300 Effective length of database: 296 Effective search space: 88800 Effective search space used: 88800 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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