Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 8501378 DvMF_2110 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Miya:8501378 Length = 316 Score = 158 bits (399), Expect = 2e-43 Identities = 98/305 (32%), Positives = 165/305 (54%), Gaps = 44/305 (14%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 A+ VSL++++G L ++GESG GK+TL R++VGL P++G+V+ DG ++F Sbjct: 11 AVDGVSLTLDRGRTLGLVGESGCGKSTLARMVVGLLPPSAGQVLLDG--------RLFAG 62 Query: 87 YRKD-----------------------VQLIPQDPYSTLPFNKTVEEILVAPILRWEKIN 123 D VQ++ QDP+S+L +TV + L + Sbjct: 63 TDGDAANGGASGHSADLAISRAEAAQLVQMVFQDPFSSLNPRRTVGAS-IGEALAVAGVP 121 Query: 124 KDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTM 183 E R ++ ++L+LV L E +YPH+ SGGQ+QR+++AR+L +P ++V DEPV+ Sbjct: 122 GPERRAKVADMLQLVGLRA--EHADRYPHEFSGGQRQRVAVARALITHPALVVCDEPVSS 179 Query: 184 VDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADL 243 +DAS++ +LN L E++ + L +FI+HD+ + H+ D + VM+ G++VE A Sbjct: 180 LDASVQAQVLNLLRELQEHMGLAYLFISHDLGVVG---HMSD--HVAVMYLGKVVEEAPR 234 Query: 244 EEILKDPLHPYTNDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDIC 298 + + P HPYT L+ P D + + ++ + GCP+ RCP MD+C Sbjct: 235 DVLFAAPAHPYTRALLASVPVRDPSRRAEHPALSGDLPSPIAPPPGCPFHPRCPQVMDVC 294 Query: 299 KNEEP 303 + + P Sbjct: 295 RRQVP 299 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: 264 Number of extensions: 11 Number of successful extensions: 5 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: 316 Length adjustment: 28 Effective length of query: 296 Effective length of database: 288 Effective search space: 85248 Effective search space used: 85248 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: 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