Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 209099 DVU0166 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >MicrobesOnline__882:209099 Length = 328 Score = 177 bits (448), Expect = 5e-49 Identities = 109/326 (33%), Positives = 178/326 (54%), Gaps = 17/326 (5%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L+V NL V + + AVNDVSF + +GE LG++GESG+GK+ +I+ I PG Sbjct: 4 LLDVQNLTVKFAL-RDEALTAVNDVSFTLGRGERLGLVGESGAGKSVTGFSIINLISKPG 62 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 I G V+F G D+ + + R + IS + Q LNPVL I ++H + Sbjct: 63 FIAGGSVLFEGNDLVTTDAETLRDIRGNRISMIFQDPMMTLNPVLTIGSQMVETILAHQK 122 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 ++ E A + L+ V + P + LK YP + SGGM+QR++IA++LL +P LI+ DEPT Sbjct: 123 MSRREAEEIALDKLRKVYIPSPEKRLKQYPHEFSGGMRQRIVIAIALLTSPSLIIADEPT 182 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q ++ L+ + + + ++ +THD+ ++Q+ ++ VMY G ++E G+T I Sbjct: 183 TALDVTIQAEIMDLLLELCESEKMGLILITHDLGVVSQVTQKIAVMYAGRIVEMGETARI 242 Query: 284 IKSPLNPYTSLLVSSIPS--------LKGEVKVINVPLDEPLVSK--EKGCPFLARCSKA 333 + P +PYT L++++P + ++ +P P +S+ CPF RC Sbjct: 243 VADPQHPYTKGLLAALPQGNSCGGGCVGKRHRLNQIPGAMPSLSEIAHGICPFHNRCELC 302 Query: 334 FGRCKEELPEIRLVYDRK---VRCHL 356 C+ P RL+ R V CHL Sbjct: 303 QDVCRTSRP--RLLPKRNGGLVACHL 326 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: 238 Number of extensions: 8 Number of successful extensions: 2 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: 328 Length adjustment: 29 Effective length of query: 333 Effective length of database: 299 Effective search space: 99567 Effective search space used: 99567 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