Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AO356_24885 AO356_24885 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24885 Length = 338 Score = 195 bits (496), Expect = 1e-54 Identities = 123/333 (36%), Positives = 173/333 (51%), Gaps = 13/333 (3%) Query: 3 EITMAKALNTALRDALRDDPRTILFGEDIG----------ALGGVFRITDGLAAEFGDER 52 +I+ +A+N AL +R D + GED+ A GGV +T GL +F R Sbjct: 4 KISYQQAINEALAQEMRRDSSVFIMGEDVAGGAGAPGENDAWGGVLGVTKGLYDQFPG-R 62 Query: 53 CFDTPLAESAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLP 112 DTPL+E +G AVG A G RPV E+ F FA +Q+++ AK R G P Sbjct: 63 VLDTPLSEIGYVGAAVGAATCGVRPVCELMFVDFAGCCLDQILNQAAKFRYMFGGKASTP 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 HKLLYSMQGEVPEELYTIPFGEANFLRDGKDVTLVSYGRMVNTAMDAARSLAGRGIDCEV 242 Query: 233 IDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVT 292 IDLRT P+D+ ++ SV +TGR VV+ EA+ +++A + ++ F L+AP+ VT Sbjct: 243 IDLRTTSPMDEDSILESVEKTGRLVVIDEANPRCSMATDVSALVAQKAFGALKAPIEMVT 302 Query: 293 GFDVPYP-PPLLERHYLPGVDRILDAVAS-LEW 323 P P LE Y+P +I AV + +EW Sbjct: 303 APHTPVPFSDALEDLYIPDAAKIEQAVLNVIEW 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: 264 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: 338 Length adjustment: 28 Effective length of query: 300 Effective length of database: 310 Effective search space: 93000 Effective search space used: 93000 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