Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_0414 Dsui_0414 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__PS:Dsui_0414 Length = 352 Score = 171 bits (434), Expect = 2e-47 Identities = 104/308 (33%), Positives = 174/308 (56%), Gaps = 19/308 (6%) Query: 19 LFKKRKF-YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIW 77 L ++RKF +A+ V+ S+ +G L ++GESG GK+T R++ L +GE+++DG + Sbjct: 38 LDRERKFVHAVDGVNFSVPKGKTLGIVGESGCGKSTTARLVARLMPADAGELIFDGEGVE 97 Query: 78 KNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLEL 137 + + K++R+++Q++ QD +++L T+ E +A R I + + + R LL+ Sbjct: 98 EFRGLRLKEFRRNLQMVFQDSFASLNPRLTIAET-IAYGPRVHGIARADHQAR--ELLDR 154 Query: 138 VKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLA 197 V L P+ F G+YPH+LSGGQ+QR++IAR+L+ +PR+++ DE V +D S++ +LN L Sbjct: 155 VGLDPSH-FAGRYPHELSGGQRQRVNIARALAFDPRLVILDEAVAALDKSVQAQVLNLLQ 213 Query: 198 EIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTND 257 E+K LT +FI+HD+ + Y +VM+ G+++E +E I P HPYT Sbjct: 214 ELKAERQLTYLFISHDLHVVHYL-----SDYVMVMYLGQVIESGPVERIYGQPAHPYTRA 268 Query: 258 LIKLTPSIDNLYKEINVKI-----NYERVEKGCPYRLRCPFAMDICKNEEPKLFKY---- 308 L+ PS+D ++ + N GC +R RCP A +C + P L Sbjct: 269 LLSAVPSMDPEHRTQASPLAGDPPNPINPPSGCRFRDRCPHAHAVCASATPALRDMGRHS 328 Query: 309 SHEVACFL 316 H AC L Sbjct: 329 EHLAACHL 336 Lambda K H 0.321 0.141 0.410 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: 300 Number of extensions: 11 Number of successful extensions: 4 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: 324 Length of database: 352 Length adjustment: 28 Effective length of query: 296 Effective length of database: 324 Effective search space: 95904 Effective search space used: 95904 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 (21.8 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