Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_024981457.1 BXU11_RS04345 ATP-binding cassette domain-containing protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_002017945.1:WP_024981457.1 Length = 253 Score = 103 bits (258), Expect = 4e-27 Identities = 81/256 (31%), Positives = 134/256 (52%), Gaps = 18/256 (7%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 ++E+ N+ + G+S+++K V+ + E G+ IIG+SGSGKT L+ ++L P Sbjct: 1 MIEIKNIEKSF--GSSKVLKGVSCL---FEAGKTNLIIGQSGSGKTVLLKSLLGIHSPE- 54 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEI--FYHEAISH 162 G + F+G I+S + E ++ L +I V Q S AL + ++E F + +H Sbjct: 55 ---VGTISFDGR-IYSDLLPEEKRELRTEIGMVFQGS--ALFDSMTVAENVGFPLKMFTH 108 Query: 163 GEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 + R +R +LK V L A K P ++SGGM++RV IA +++ NPK + DEP Sbjct: 109 NSPSETR--DRVDFVLKRVNLIDAH--KKLPSEISGGMQKRVAIARAIVNNPKYLFCDEP 164 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 S LD ++ LIK I +E +T V THD+ ++ +I +L + G +G EE Sbjct: 165 NSGLDPNTSTIIDNLIKEITEEYNITTVINTHDMNSVMEIGENILFLKNGIKEWQGTKEE 224 Query: 283 IIKSPLNPYTSLLVSS 298 I ++ + SS Sbjct: 225 IFRTDNQAIVDFVYSS 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: 183 Number of extensions: 6 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: 253 Length adjustment: 27 Effective length of query: 335 Effective length of database: 226 Effective search space: 75710 Effective search space used: 75710 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 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