Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 7025500 Shewana3_2654 ABC transporter related (RefSeq)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__ANA3:7025500 Length = 261 Score = 135 bits (341), Expect = 9e-37 Identities = 83/256 (32%), Positives = 144/256 (56%), Gaps = 13/256 (5%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVND----VSFGVEKGEILGIIGESGSGKTTLISAILRAI 100 +L+V++L YD G + ND VSF + +GE L I+GE+GSGK+TL ++ A Sbjct: 5 LLKVNDLFKRYDTGYKGFTRQYNDALAPVSFELNRGETLAIVGEAGSGKSTLARILVGAE 64 Query: 101 RPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAI 160 G G++ F G + S I + +L I + Q +LNP L I ++ Sbjct: 65 PRSG----GEIYFEGEALDSRNIKQRCRL----IRMIFQDPNTSLNPRLTIGQLLDEPLR 116 Query: 161 SHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMD 220 + E K + + L+ VGL P YP +S G KQRV +A +L+LNPK+I+ D Sbjct: 117 FNTELSAKERSGQVIDTLRKVGLLPEHA-DFYPHMISEGQKQRVAVARALMLNPKIIIAD 175 Query: 221 EPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKT 280 E +ALD+ + +L L+ + +++G++ ++V+H++ I ++++++V++KG ++E+ T Sbjct: 176 EALTALDLSVRSQILNLLLKLQKDLGLSYIFVSHNLNIIRHVSDKIMVLHKGVMVEKAPT 235 Query: 281 EEIIKSPLNPYTSLLV 296 E+I SP + YT L+ Sbjct: 236 EQIFNSPQHEYTQRLI 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: 235 Number of extensions: 12 Number of successful extensions: 1 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