Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_086509537.1 BZY95_RS08640 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_002151265.1:WP_086509537.1 Length = 349 Score = 196 bits (499), Expect = 6e-55 Identities = 110/316 (34%), Positives = 185/316 (58%), Gaps = 4/316 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L V +L V + + ++ A++DVSF + GE+LG++GESG+GK+ +A++R + PPG Sbjct: 14 VLSVRHLRVEFPTRHGTLV-ALDDVSFDIAPGEVLGVVGESGAGKSMTGNAVIRLLEPPG 72 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 I +G+V+ +G I + + F L + I + Q +LNP+ + + +H Sbjct: 73 HIAAGEVLLSGQRIDDLPEERFVPLRGRHIGMIFQDPLTSLNPLFSVGDQLIETIRAHLP 132 Query: 165 ADKKRVIERASELLKLVGLD-PARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 +++ E A +LL+ VG+ P + YP Q SGGM+QRV+IAL+L P+ I+ DEPT Sbjct: 133 MNEREAREEALKLLREVGIPAPENRIDSYPHQFSGGMRQRVVIALALAARPEFIIADEPT 192 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +L L+K + + G ++ VTHD+ IA+ A+R+ VMY G ++E G +E+ Sbjct: 193 TALDVSVQAQILALLKRLCADHGTAVMLVTHDMGVIAETADRVAVMYAGRLIEIGPVDEV 252 Query: 284 IKSPLNPYTSLLVSSIPSLKGEV-KVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341 I+ P +PYT L++SIP + + ++ + P L + GC F RC A RC++E Sbjct: 253 IRHPQHPYTKGLMASIPGIAKRLDRLYQIEGAMPRLAAIPSGCAFNPRCPHAQQRCRDER 312 Query: 342 PEIRLVYDRKVRCHLY 357 P++ + C L+ Sbjct: 313 PDLMPAGGSRAACWLH 328 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: 260 Number of extensions: 8 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: 349 Length adjustment: 29 Effective length of query: 333 Effective length of database: 320 Effective search space: 106560 Effective search space used: 106560 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 24 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