Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 3607113 Dshi_0535 Transketolase central region (RefSeq)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Dino:3607113 Length = 327 Score = 243 bits (620), Expect = 5e-69 Identities = 141/318 (44%), Positives = 182/318 (57%), Gaps = 2/318 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 + + T AL AL +A+ D I+ GE++G GG + +T L EFG ER DTP++E Sbjct: 3 VQQTTYRDALRLALSEAMTKDENVIVMGEEVGRYGGAYGVTKDLIKEFGPERVIDTPISE 62 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 +AI+G AVG AM G RPV E+ + F +QL + AK+R G IG+P+ +R G Sbjct: 63 AAIVGAAVGAAMTGLRPVAELMYVDFIGMTMDQLANQAAKIRYMFGGQIGVPMVLRTQGG 122 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 G HS S E Y M TPGL + PAT DAY LLR+S+ PDPVVF+E K LY K Sbjct: 123 TGRSAGAQHSQSLEGYIMHTPGLRLAMPATVEDAYHLLRQSLQQPDPVVFIEHKGLYTMK 182 Query: 181 EALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEA-AAEHGWDLEVIDLRTLM 239 AL G A + R G ++ Y V ALEAAE A HG ++ V+DLRTL Sbjct: 183 GALDPDAAPAGWGEATVLREGDDLVIVTYSRQVHHALEAAETLAGAHGINVTVVDLRTLN 242 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 PLD T+ V GRA+VV E G AE++ARITE CF LE PV RV G D+P Sbjct: 243 PLDFDTIRPLVEAAGRAMVVSEGVMTCGVAAELSARITEECFDFLEEPVVRVAGEDIPIS 302 Query: 300 -PPLLERHYLPGVDRILD 316 PLLE++ +P + I+D Sbjct: 303 VSPLLEQNSVPTPELIVD 320 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: 287 Number of extensions: 12 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: 327 Length adjustment: 28 Effective length of query: 300 Effective length of database: 299 Effective search space: 89700 Effective search space used: 89700 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