Align CbtB, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate SM_b21038 SM_b21038 oligopeptidemurein peptide ABC transporter permease
Query= TCDB::Q97VF8 (333 letters) >FitnessBrowser__Smeli:SM_b21038 Length = 325 Score = 123 bits (308), Expect = 7e-33 Identities = 88/255 (34%), Positives = 130/255 (50%), Gaps = 3/255 (1%) Query: 78 YIWNTLHGNLGFSIISNVPVAELIAVALPWTLFIVVTSILISFFLGIRLGQKLGYLRGTK 137 +I N + GN G S I ++P EL+ LP TL + ++LI+ LG LG G GT Sbjct: 70 FIGNVVSGNFGTSYIYHLPAFELVMSKLPATLELASIAMLIAAPLGTGLGLLAGRRSGTL 129 Query: 138 TD-SVATVSLSILRSVPIYIYAVLLIYILAFIYHIFPTGGAYSIHVTPGFNLPFI-ASVL 195 D ++ S+S L S+P + A++LI + A + FP+GG G F+ A+ L Sbjct: 130 FDRTMVKASVSAL-SIPSFWLAMMLILVGAILTGWFPSGGRGLTASFLGQEWSFLTANGL 188 Query: 196 YHAFLPILTLTIVNLVGWILQMRANTIYVLGEDFVNFAEISGVKKDIIEKKYIGKNAILP 255 +H LP L L I N+ R+ TI V D+ F G+ I ++ N +P Sbjct: 189 WHLVLPALALAIPNIALIARLSRSGTIEVENLDYTRFCRAKGLSARRILFRHTLPNISVP 248 Query: 256 LYTSLIISIGFSFSGSVFVEQTFSYPGVGNLLINSITSNDYPTEMGVFIIIIVAVIVGNL 315 + T + + G + +V VE FS+PGVG LLI+SI D P M +I VA + N Sbjct: 249 IVTIIGLQFGGMLAFAVVVETIFSWPGVGKLLIDSIQLLDRPVVMATLTVIAVAFVALNA 308 Query: 316 IADLTYSFLDPRAKV 330 + DL Y+ LDPR ++ Sbjct: 309 LVDLFYAVLDPRVRL 323 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: 214 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: 333 Length of database: 325 Length adjustment: 28 Effective length of query: 305 Effective length of database: 297 Effective search space: 90585 Effective search space used: 90585 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