Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 209098 DVU0165 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >MicrobesOnline__882:209098 Length = 337 Score = 184 bits (468), Expect = 2e-51 Identities = 108/297 (36%), Positives = 169/297 (56%), Gaps = 21/297 (7%) Query: 18 GLFKKRKF-YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNI 76 G+ +KR +A+ DVS ++N+G+ L V+GESG GK+TL R ++GL +P SGE+ Y I Sbjct: 32 GIVRKRTVVHAVNDVSFTINEGETLSVVGESGCGKSTLARTVIGLYRPNSGEIHYRDRRI 91 Query: 77 WKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK--INKDELRKRLINL 134 YR +Q++ QDPY++L V +IL PI R+ I + E+ R+ + Sbjct: 92 DHLSDTEMLPYRTRMQMVFQDPYASLNPRMRVNQILEEPI-RFHNPGIGEGEVLDRVAAV 150 Query: 135 LELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILN 194 +E V + P + +YPH+ SGGQ+QR+SIAR+L+V+P IVADEP++ +D S++ +LN Sbjct: 151 MEQVGINPV--WATRYPHEFSGGQRQRISIARALAVDPEFIVADEPISALDVSIQAQVLN 208 Query: 195 TLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPY 254 + +++ + NLT +FI+HD+ + + VM+ G + E A E++ P HPY Sbjct: 209 LMMDMQEQRNLTYLFISHDLSVVEHI-----STRVAVMYLGSLCELATSEDLFGSPRHPY 263 Query: 255 TNDLIKLTPSID-------NLYKEINVKINYERVEKGCPYRLRCPFAMDICKNEEPK 304 T L+ P I L ++ IN + GC + RCP A C NE P+ Sbjct: 264 TQALLSAIPRIGQKGLKHIRLSGDVPTPIN---LPSGCVFHGRCPHADKRCMNEVPR 317 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: 305 Number of extensions: 20 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: 337 Length adjustment: 28 Effective length of query: 296 Effective length of database: 309 Effective search space: 91464 Effective search space used: 91464 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