Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3697 PGA1_262p01010 dipeptide transport ATP-binding protein DppD
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Phaeo:GFF3697 Length = 330 Score = 194 bits (493), Expect = 3e-54 Identities = 115/319 (36%), Positives = 188/319 (58%), Gaps = 14/319 (4%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L V +L V + + A+N +SF + KGE LGI+GESG+GK+ +++ + PG Sbjct: 3 LLSVRDLTVKFAM-RDHTVTALNQISFDLGKGERLGIVGESGAGKSITGFSLMNLLSRPG 61 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISE-----IFYHEA 159 I SG+++F DI ++ E RK+ ++ + Q LNPVL I + + H + Sbjct: 62 FIDSGQILFGDKDIVKLSDAEMRKIRGNRMAMIFQDPMVTLNPVLTIGQQMVETLKAHRS 121 Query: 160 ISHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILM 219 +S EA++ +++ L ++ P L YP +LSGGM+QR++IA++LLL+P+LI+ Sbjct: 122 LSKAEAEQIAILK----LREVYIPSPEERLNQYPHELSGGMRQRIIIAMALLLDPELIIA 177 Query: 220 DEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGK 279 DEPT+ALD+ Q +++L+ + Q V ++ +THD+ ++Q+ R LVMY G ++E G Sbjct: 178 DEPTTALDVTIQADIMELLLELCQSNKVGLILITHDLGVVSQMTERTLVMYAGRLIEAGP 237 Query: 280 TEEIIKSPLNPYTSLLVSSIP--SLKGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGR 336 T EII P +PYT L++++P +L G+ ++ +P + P L S GCPF RC A Sbjct: 238 TREIINDPQHPYTQGLINALPQQTLPGQ-RLKQIPGNMPGLASIPPGCPFSPRCEYAVDH 296 Query: 337 CKEELPEIRLVYDRKVRCH 355 C++ LPE +V CH Sbjct: 297 CRKVLPETVSYRQVEVACH 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: 250 Number of extensions: 7 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: 330 Length adjustment: 29 Effective length of query: 333 Effective length of database: 301 Effective search space: 100233 Effective search space used: 100233 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