Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AO353_25155 AO353_25155 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25155 Length = 339 Score = 201 bits (510), Expect = 3e-56 Identities = 127/333 (38%), Positives = 172/333 (51%), Gaps = 13/333 (3%) Query: 3 EITMAKALNTALRDALRDDPRTILFGEDIG----------ALGGVFRITDGLAAEFGDER 52 +I+ +A+N AL +R DP + GED+ A GGV +T GL +F R Sbjct: 4 KISYQQAINEALAQEMRRDPSVFIMGEDVAGGAGAPGENDAWGGVLGVTKGLYHQFPG-R 62 Query: 53 CFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLP 112 DTPL+E +G AVG A G RPV E+ F FA +Q+++ AK R G P Sbjct: 63 VLDTPLSELGYVGAAVGAATCGVRPVCELMFVDFAGCCLDQILNQAAKFRYMFGGKASTP 122 Query: 113 LTIRIPYGGGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLE 172 L IR G G+ HS + PGL VV P++ DA LL ++I DPV+F E Sbjct: 123 LVIRTMVGAGLRAAAQHSQMLTSLWTHIPGLKVVCPSSPYDAKGLLIQAIRDNDPVIFCE 182 Query: 173 PKRLYWRKEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEV 232 K LY + + + T P G A R G TL++YG V TA++AA A G D EV Sbjct: 183 HKMLYSMQGEVPEELYTIPFGEANFLRDGKDVTLVSYGRTVNTAMDAARNLAARGIDCEV 242 Query: 233 IDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVT 292 IDLRT PLD+ ++ SV +TGR VV+ EA+ +I+A + ++ F L+AP+ VT Sbjct: 243 IDLRTTSPLDEDSILESVEKTGRLVVIDEANPRCSMATDISALVAQKAFASLKAPIEMVT 302 Query: 293 GFDVPYP-PPLLERHYLPGVDRILDAVASL-EW 323 P P LE Y+P +I AV L EW Sbjct: 303 APHTPVPFSDALEDLYIPDAAKIESAVLKLIEW 335 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: 274 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: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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