Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_0415 Dsui_0415 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__PS:Dsui_0415 Length = 326 Score = 172 bits (437), Expect = 9e-48 Identities = 103/313 (32%), Positives = 171/313 (54%), Gaps = 5/313 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 ++ + +L V ++ +R A+N VS + +GE+LG++GESGSGK+ + +LR Sbjct: 5 LVSIQDLTVQFN--GARRASALNQVSLELGQGEVLGLLGESGSGKSVTLRTLLRLHPERH 62 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 +G++ +G D+ ++ E + +S V Q A +PV I + H Sbjct: 63 TRTAGRIRVDGQDVLALRGRELDRYRGGTVSMVFQEPGLAFDPVYTIGQQISEAVRVHEG 122 Query: 165 ADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 D+ RA +L+ V + AR YP +LSGGM+QR MIAL+L PKL+L DEPT Sbjct: 123 VDQATAAARALAMLERVQIPQARRRFDAYPHELSGGMRQRAMIALALACKPKLLLADEPT 182 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD Q +L L++ + +E G+++++VTHDI ++A+R+ VMY G ++E+G ++ Sbjct: 183 TALDATVQIQILLLLRELQRETGMSVIFVTHDIGAAVEVADRIAVMYAGRIVEQGPVGQL 242 Query: 284 IKSPLNPYT-SLLVSSIPSLKGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341 ++ P +PYT LL +++ + +P P L + GC F RCS A RC ++ Sbjct: 243 VRQPCHPYTRGLLAATVGHEHRGRPLEAIPGSPPDLAALPPGCSFAPRCSHASERCHRDI 302 Query: 342 PEIRLVYDRKVRC 354 P + R + C Sbjct: 303 PPLEQQGARTLAC 315 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: 225 Number of extensions: 6 Number of successful extensions: 4 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: 326 Length adjustment: 29 Effective length of query: 333 Effective length of database: 297 Effective search space: 98901 Effective search space used: 98901 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