Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Miya:8500263 Length = 358 Score = 176 bits (447), Expect = 7e-49 Identities = 101/311 (32%), Positives = 167/311 (53%), Gaps = 11/311 (3%) Query: 45 ILEVHNLNVIY------DEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILR 98 +L+V +L+V + D ++AV +SF + G L ++GESG GK+ A+LR Sbjct: 17 LLDVRDLSVEFPGRPEADGTPGAPLRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLR 76 Query: 99 AIRPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHE 158 + PG++ SG V G ++ ++ E R + + IS + Q +LNPV + E Sbjct: 77 LVPEPGRVASGSVRLEGRELLTLPEPEMRGVRGRSISMIFQEPMTSLNPVFRVGEQIAEG 136 Query: 159 AISHGEADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217 H + RA +LL+ VG+ P + +P Q+SGGM+QRVMIA++L +P+L+ Sbjct: 137 VRLHLGLSRSDAAARAVDLLRQVGIPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLL 196 Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277 + DEPT+ALD+ Q +L+L++++ G +++ +THD+ +A+ A+ + VMY G +ME Sbjct: 197 IADEPTTALDVTIQRQILRLMRDLAAHRGASVLLITHDLGVVAETADHVAVMYAGRIMEH 256 Query: 278 GKTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVP----LDEPLVSKEKGCPFLARCSKA 333 + PL+PY L+ S+P + + PL + GC F RC A Sbjct: 257 ASVGDFFARPLHPYAQGLMRSVPQAVSGPRAERLSAIPGTVPPLWALPSGCTFRDRCPHA 316 Query: 334 FGRCKEELPEI 344 F RC E+ P + Sbjct: 317 FARCAEQEPPL 327 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: 262 Number of extensions: 6 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: 358 Length adjustment: 29 Effective length of query: 333 Effective length of database: 329 Effective search space: 109557 Effective search space used: 109557 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