Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 6938692 Sama_2795 transketolase, central region (RefSeq)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__SB2B:6938692 Length = 761 Score = 130 bits (328), Expect = 8e-35 Identities = 93/297 (31%), Positives = 136/297 (45%), Gaps = 23/297 (7%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 + M K +N L + + ++ GED+G GGV+ +T L FG R +T L E++I Sbjct: 402 VHMGKLINLTLTELMASHDNVVVCGEDVGKKGGVYHVTSRLVERFGPSRVINTLLDETSI 461 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRI---PYG 120 LG A GMA G P+ E+QF A+ + A +Q+ A L + G P+ IRI Y Sbjct: 462 LGLATGMAHNGLLPIPEIQFLAYVHNAEDQIRGEAATLPFFSNGQYTNPMVIRIAGLAYQ 521 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSI----ASPDPVVFLEPKRL 176 G GG H+D+S + PGL + P+ ADA +LR + V+FLEP L Sbjct: 522 KGFGG-HFHNDNSFTVFRDIPGLILACPSNGADAQGMLRECVRLAREEQRLVIFLEPIAL 580 Query: 177 YWRKEALGLPVDT--------------GPLGSAVIRRHGTHATLIAYGPAVTTALEAAEA 222 Y ++ L P D+ P G G +I+YG + +A +A Sbjct: 581 YMTRD-LHEPGDSLWAAQYVPEREATPLPFGEPGRFGEGKDLCIISYGNGYYLSRQAEKA 639 Query: 223 AAEHGWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITER 279 AE G D ++DLR L PL++A +C +VV E I + ER Sbjct: 640 LAEAGIDCTLVDLRYLAPLNEAAICDIAANCRHVLVVDECRRSGSVSEAIVTALHER 696 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: 548 Number of extensions: 20 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: 761 Length adjustment: 34 Effective length of query: 294 Effective length of database: 727 Effective search space: 213738 Effective search space used: 213738 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: 52 (24.6 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