Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF205 HP15_204 oligopeptide/dipeptide ABC transporter, ATPase subunit
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Marino:GFF205 Length = 336 Score = 184 bits (467), Expect = 3e-51 Identities = 103/307 (33%), Positives = 176/307 (57%), Gaps = 26/307 (8%) Query: 21 KKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNK 80 K+ +A+ V L + +G+ L V+GESG GK+T+ R ++GL P++GE+ YDG I + Sbjct: 35 KQEAVHAINGVDLEVQKGEALCVVGESGCGKSTVARTVMGLLSPSAGEIHYDGQRIDNLE 94 Query: 81 RKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPIL----RWEKINKDELRKRLINLLE 136 RK YR+ +Q+I Q+PY++L T+++ L PI W + ++R ++ ++ Sbjct: 95 RKDSLPYRRKMQMIFQNPYASLNPRMTIQQTLEEPIRFHHPDWSPV---QVRDKIHEVMH 151 Query: 137 LVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTL 196 V + +++ ++ H+ SGGQ+QR++IAR+L+V+P IVADEP++ +D S++ +LN L Sbjct: 152 SVGID--QDWGNRFGHEFSGGQRQRIAIARALAVDPEFIVADEPISALDVSIQAQVLNLL 209 Query: 197 AEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTN 256 + + LT +FITHD+ + +F VM+ GR+ E AD + + P HPYT Sbjct: 210 MDAQESRGLTYLFITHDLAVVEHF-----GTRVAVMYLGRVCELADTKTLFSAPRHPYTQ 264 Query: 257 DLIKLTPSIDN-------LYKEINVKINYERVEKGCPYRLRCPFAMDICKNEEPKLFKY- 308 L+ P +++ L E+ +N + GC + RCP+A + C+ E P+L Sbjct: 265 ALLSAIPKLEDDRPNHIRLKGEVPTPVN---LPSGCVFHGRCPYANERCRQELPQLITTD 321 Query: 309 -SHEVAC 314 +VAC Sbjct: 322 GGTQVAC 328 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: 283 Number of extensions: 15 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: 336 Length adjustment: 28 Effective length of query: 296 Effective length of database: 308 Effective search space: 91168 Effective search space used: 91168 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