Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate 3608767 Dshi_2159 Transketolase central region (RefSeq)
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Dino:3608767 Length = 451 Score = 215 bits (548), Expect = 1e-60 Identities = 125/320 (39%), Positives = 177/320 (55%), Gaps = 2/320 (0%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M +T+ +AL A+ + +R + L GE++ G ++I+ GL EFG +R DTP+ E Sbjct: 126 MKSMTVREALRDAMAEEMRRNENVFLMGEEVAEYQGAYKISQGLLDEFGSKRVIDTPITE 185 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 G AVG A G P+VE FA A +Q+++ AK + G +G P+ R P G Sbjct: 186 HGFAGLAVGAAFGGLNPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGCPIVFRGPNG 245 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRK 180 HS S +Y PGL V P +A+DA LL+ +I P+PV+FLE + LY R Sbjct: 246 AAARVAAQHSQDSAAWYAHIPGLKVAMPYSASDAKGLLKSAIRDPNPVIFLENEILYGRS 305 Query: 181 EALGLPVD-TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239 + + D T P G A I R G T++++G +T ALEAA+ A+ G EV+DLRTL Sbjct: 306 FEVPMIDDYTVPFGKARIWREGRDVTIVSFGIGMTYALEAADRLAKDGISAEVVDLRTLR 365 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPYP 299 PLD TV ASV++T R V V E A G I+A + + F +L+APV +TG DVP P Sbjct: 366 PLDTETVIASVQKTNRCVTVEEGFPVASIGNHISAVLMQEAFDYLDAPVINLTGKDVPMP 425 Query: 300 -PPLLERHYLPGVDRILDAV 318 LE+ L D +++AV Sbjct: 426 YAANLEKLALVTTDEVIEAV 445 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: 379 Number of extensions: 25 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: 451 Length adjustment: 30 Effective length of query: 298 Effective length of database: 421 Effective search space: 125458 Effective search space used: 125458 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: 50 (23.9 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