Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate PP_0878 PP_0878 dipeptide ABC transporter, binding subunit
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Putida:PP_0878 Length = 322 Score = 185 bits (469), Expect = 1e-51 Identities = 109/309 (35%), Positives = 174/309 (56%), Gaps = 14/309 (4%) Query: 13 FEDKVGLFKKRKFY-ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVY 71 +E GLFK AL VS + G L V+GESG GK+TL R + +++P+SG + Sbjct: 14 YEVSRGLFKGHALVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIEEPSSGSLQI 73 Query: 72 DGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRL 131 G + + K+ R+DVQ++ Q PY++L + + + L P+L ++K E R ++ Sbjct: 74 AGTEVKGASKAERKQLRRDVQMVFQSPYASLNPRQKIGDQLAEPLLINTSLSKAERRDKV 133 Query: 132 INLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIG 191 ++E V L P E +YPH SGGQ+QR+++AR++ + P+++VADEP + +D S++ Sbjct: 134 QKMMEQVGLRP--EHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQ 191 Query: 192 ILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPL 251 +LN +++ N VFI+H++ + R H+ D+ +VM+ GR E E+I PL Sbjct: 192 VLNLFMDLQKEFNTAYVFISHNLAVVR---HVADQ--VLVMYLGRPAEMGPKEDIYAKPL 246 Query: 252 HPYTNDLIKLTPSI--DNLYKEINV---KINYERVEKGCPYRLRCPFAMDICKNEEPKLF 306 HPYT L+ TP+I D L +I + N GC + RCP+A + C E P L Sbjct: 247 HPYTQALLSATPAIHPDPLKPKIRIVGELPNPLNPPDGCAFHKRCPYATERCAKEVPALR 306 Query: 307 KYS-HEVAC 314 + S +VAC Sbjct: 307 QVSTRQVAC 315 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: 276 Number of extensions: 14 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: 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