Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 3610414 Dshi_3795 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Dino:3610414 Length = 331 Score = 182 bits (463), Expect = 8e-51 Identities = 116/323 (35%), Positives = 182/323 (56%), Gaps = 22/323 (6%) Query: 45 ILEVHNLNVIYDEG----NSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAI 100 +L HNL + G N R+++AV+DV+F V GE LG++GESG GK+T +++ + Sbjct: 10 VLSAHNLVKHFPLGGWGKNRRVVRAVDDVTFEVAPGETLGVVGESGCGKSTTARLLVQLL 69 Query: 101 RPPGKIISGKVIFNG-MDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159 SG+V F G + M + EFR+ + V Q S +LNP + + + Sbjct: 70 GAD----SGEVRFQGHVAGTEMPLKEFRR----HVQMVFQDSYASLNPRMSMLDAIAFGP 121 Query: 160 ISHG--EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217 HG EA+ +R+ A +LL VGLDP+R YP +LSGG +QRV IA +L P++I Sbjct: 122 TVHGVSEAEAQRI---ARDLLDRVGLDPSRFGPRYPHELSGGQRQRVNIARALAFQPEVI 178 Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277 ++DE SALD + +L L+ ++ +E +T V+++HD+ + +++R++VMY G V E Sbjct: 179 VLDEAVSALDKSVEAQVLNLLMDLKRERNLTYVFISHDLNVVRHVSDRVMVMYLGEVAEI 238 Query: 278 GKTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVPL--DEP-LVSKEKGCPFLARCSKAF 334 G T E+ P +PYT L++++PSL + + PL D P + GC F RC++AF Sbjct: 239 GPTAEMYADPRHPYTRALLAAMPSLDPDRRTTEAPLSGDPPNPIDPPSGCRFHTRCAEAF 298 Query: 335 GRCKEELP-EIRLVYDRKVRCHL 356 G C + P +R+ CHL Sbjct: 299 GACSAQRPSNLRVGAGHYASCHL 321 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: 261 Number of extensions: 14 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: 331 Length adjustment: 29 Effective length of query: 333 Effective length of database: 302 Effective search space: 100566 Effective search space used: 100566 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