Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AZOBR_RS04800 AZOBR_RS04800 pyruvate dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__azobra:AZOBR_RS04800 Length = 343 Score = 207 bits (528), Expect = 2e-58 Identities = 132/327 (40%), Positives = 173/327 (52%), Gaps = 12/327 (3%) Query: 3 EITMAKALNTALRDALRDDPRTILFGEDI----------GALGGVFRITDGLAAEFGDER 52 +I+M A+N AL +R DP IL GEDI A GGV +T GL A+ GD R Sbjct: 4 KISMKTAINEALDLEMRRDPTVILMGEDIVGGTGAPGEDDAWGGVLGVTKGLFAKHGD-R 62 Query: 53 CFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLP 112 DTPL+ESA +G A+G A G RPV E+ F F F+Q+ + AK R G P Sbjct: 63 LLDTPLSESAYIGAAIGAATCGMRPVAELMFMDFMGVCFDQIFNQAAKFRYMFGGKAETP 122 Query: 113 LTIRIPYGGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLE 172 + IR G G HS + PGL VV P+ A DA LL +SI DPV+F E Sbjct: 123 VVIRGMVGAGFRAAAQHSQMLTPLFTHIPGLKVVCPSNAYDAKGLLIQSIRDNDPVIFCE 182 Query: 173 PKRLYWRKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEV 232 K LY + + P G A + R G H T+++YG V A+EAA+A A+ + EV Sbjct: 183 HKNLYGHETEVPAESYAIPFGEANVLRDGDHVTIVSYGLTVHRAMEAADALAKDKVEAEV 242 Query: 233 IDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVT 292 IDLRTL P+D T+ SV RTGR VVV EAH +I+A + + F L++ ++ VT Sbjct: 243 IDLRTLSPIDWDTIIDSVERTGRLVVVDEAHPRCNLATDISAFVAQNAFGALKSGIQMVT 302 Query: 293 GFDVPYP-PPLLERHYLPGVDRILDAV 318 P P P LE Y+P + + AV Sbjct: 303 PPHTPVPFSPSLEDLYIPSAEAVAAAV 329 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: 326 Number of extensions: 17 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: 343 Length adjustment: 28 Effective length of query: 300 Effective length of database: 315 Effective search space: 94500 Effective search space used: 94500 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 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