Align CbtB, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 3609627 Dshi_3010 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q97VF8 (333 letters) >FitnessBrowser__Dino:3609627 Length = 339 Score = 191 bits (486), Expect = 2e-53 Identities = 114/331 (34%), Positives = 176/331 (53%), Gaps = 4/331 (1%) Query: 5 WLIRRLASVIIAIFVTIVISWALLEFSPYSPANYIMQFINPQDFAQKPELYASLIDYLNT 64 +LI R + ++ +F+ + W + FSP PA ++ + A +++ L Sbjct: 8 YLINRTITFVLTVFIAATLIWLIPRFSPVDPAEIMLSRMAAGGGAVADS--EAILAQLRA 65 Query: 65 LRPHGNPLI-NAVNYIWNTLHGNLGFSIIS-NVPVAELIAVALPWTLFIVVTSILISFFL 122 +PLI + Y+ N L NLG S S PV+ LIA ALPWTL +++ S++I+F + Sbjct: 66 DFGLNDPLIVQYLKYMGNLLTFNLGISTASFPTPVSVLIAQALPWTLGLMILSVVITFVI 125 Query: 123 GIRLGQKLGYLRGTKTDSVATVSLSILRSVPIYIYAVLLIYILAFIYHIFPTGGAYSIHV 182 G LG + + R K V + I S+P + +LL+YI + P G+Y + V Sbjct: 126 GNALGAFMVWERTPKIWKVVIPTFMIFTSIPPILSGLLLMYIFSITLRWLPLTGSYGLTV 185 Query: 183 TPGFNLPFIASVLYHAFLPILTLTIVNLVGWILQMRANTIYVLGEDFVNFAEISGVKKDI 242 PG++ FI+SV+ H LP L++ +V W L MR I V GED+VN A+ G+K Sbjct: 186 EPGWDWAFISSVIEHGTLPALSIIVVTFGFWTLGMRGLMISVQGEDYVNLAKAKGLKPRY 245 Query: 243 IEKKYIGKNAILPLYTSLIISIGFSFSGSVFVEQTFSYPGVGNLLINSITSNDYPTEMGV 302 + KY+ +NAILP T+ + IG SG + VE+ F Y G+G LL ++I D+ GV Sbjct: 246 VLYKYMVRNAILPQITAFALKIGLLVSGQILVERIFGYNGMGKLLYDAILDQDFAVIQGV 305 Query: 303 FIIIIVAVIVGNLIADLTYSFLDPRAKVGEE 333 III+ + + DL Y +DPR ++ EE Sbjct: 306 SYIIILMTALSVFLVDLIYPLIDPRIRLSEE 336 Lambda K H 0.327 0.144 0.429 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: 289 Number of extensions: 11 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: 333 Length of database: 339 Length adjustment: 28 Effective length of query: 305 Effective length of database: 311 Effective search space: 94855 Effective search space used: 94855 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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