Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 5210055 Shew_2502 ABC transporter-related protein (RefSeq)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__PV4:5210055 Length = 261 Score = 132 bits (331), Expect = 1e-35 Identities = 74/232 (31%), Positives = 136/232 (58%), Gaps = 9/232 (3%) Query: 65 AVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMTID 124 A+ +SF + +GE L I+GE+GSGK+TL ++ A + G+++F G + S + Sbjct: 29 ALEPISFELNRGETLAIVGETGSGKSTLARILVGAEQRT----DGEILFEGEALESRNLK 84 Query: 125 EFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVGLD 184 + +L I + Q +LNP L + E+ + + DK+ + + L+ VGL Sbjct: 85 QRCRL----IRMIFQDPNTSLNPRLTVGELLDEPLRFNTDLDKQARFAQVVDTLRKVGLL 140 Query: 185 PARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNINQE 244 P YP +S GMKQRV +A +L+LNPK+I+ DE +ALD+ + +L L+ + QE Sbjct: 141 PEHA-DFYPHMISEGMKQRVAVARALMLNPKIIIADEALTALDLSVRSQILNLLLKLQQE 199 Query: 245 MGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLV 296 MG++ ++V+H++ I +++++V+++G ++E+ TE++ +P + YT L+ Sbjct: 200 MGLSYIFVSHNMNIIRHFSDKIMVLHQGKMVEKATTEKLFNAPEHEYTQRLI 251 Lambda K H 0.319 0.138 0.391 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: 233 Number of extensions: 10 Number of successful extensions: 3 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: 362 Length of database: 261 Length adjustment: 27 Effective length of query: 335 Effective length of database: 234 Effective search space: 78390 Effective search space used: 78390 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