Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate PfGW456L13_5057 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5057 Length = 322 Score = 153 bits (387), Expect = 5e-42 Identities = 103/327 (31%), Positives = 177/327 (54%), Gaps = 25/327 (7%) Query: 1 MGLMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60 M L+E+K ++V F DK + + L +++G++L ++GESG+GK+ ++G Sbjct: 1 MSLLEIKNLNVRFGDK------NATPVVDGLDLQVDKGEVLAIVGESGSGKSVTMMALMG 54 Query: 61 L-QKP---TSGEVVYDGYNIWK-NKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAP 115 L + P T+ + +DG N+ K N R+ + KD+ ++ QDP + L + TV + Sbjct: 55 LIEHPGIVTADALNFDGKNMLKLNNRQRRQIVGKDLSMVFQDPMTALNPSYTVG-FQIEE 113 Query: 116 ILRWE-KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRI 174 +LR K++ RKR I LLE V++ A + YPHQLSGG QR++IA +++ P++ Sbjct: 114 VLRLHLKMSGKAARKRAIELLEKVEIPGAASRMDAYPHQLSGGMSQRVAIAMAIAGEPKL 173 Query: 175 IVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFA 234 ++ADEP T +D +++ I++ L ++ N+ +V ITHD+ + VM+A Sbjct: 174 LIADEPTTALDVTIQAQIMDLLLALQKEQNMGLVLITHDLAVVAE-----TAQRVCVMYA 228 Query: 235 GRIVERADLEEILKDPLHPYTNDLIKLTPSIDNLYKEIN-----VKINYERVEKGCPYRL 289 G+ VE + ++ P HPY+ L+K P ++ V Y+R +GC Sbjct: 229 GQAVEVGQVPQLFDIPAHPYSEALLKAIPEHSLGASRLSTLPGIVPGRYDR-PQGCLLSP 287 Query: 290 RCPFAMDICKNEEPKLFKYSHEVA-CF 315 RCP+ D C+ + P L + S+ +A CF Sbjct: 288 RCPYVKDNCRQQRPALDQKSNSLARCF 314 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: 287 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 324 Length of database: 322 Length adjustment: 28 Effective length of query: 296 Effective length of database: 294 Effective search space: 87024 Effective search space used: 87024 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