Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Pedo557:CA265_RS16020 Length = 250 Score = 108 bits (270), Expect = 2e-28 Identities = 78/236 (33%), Positives = 125/236 (52%), Gaps = 13/236 (5%) Query: 67 NDVSFGV----EKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 NDV G+ E+G IIG SGSGKTTL+ ++ +P SG V+++G D MT Sbjct: 14 NDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPD----SGSVLYDGRDFTPMT 69 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182 ++ R + K+I + Q S AL + + E + +K +ER L+ V Sbjct: 70 YEQ-RIEVRKEIGMLFQGS--ALFDSMTVEENIMFPLNMFTDQSRKEKLERVDFCLERVN 126 Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242 L A K++P +LSGGMK+RV IA ++ +NPK + DEP S LD ++ +LI+ I Sbjct: 127 L--AGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNSGLDPKTSIVIDELIQEIT 184 Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298 +E T + VTHD+ ++ I + +L +++G EG +EI + + + +S Sbjct: 185 EEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEGSNKEIAHTDIKELNDFVFAS 240 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: 192 Number of extensions: 7 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: 250 Length adjustment: 27 Effective length of query: 335 Effective length of database: 223 Effective search space: 74705 Effective search space used: 74705 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