Align CbtC, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate PP_3221 PP_3221 ABC transporter, permease protein
Query= TCDB::Q97VF6 (290 letters) >FitnessBrowser__Putida:PP_3221 Length = 302 Score = 98.6 bits (244), Expect = 2e-25 Identities = 66/225 (29%), Positives = 112/225 (49%), Gaps = 8/225 (3%) Query: 20 RVGLIITVFYILIAIFGQIIFPKTYSLPP---SPTTIFMPPQLSNFYLIFGTGPFAESIL 76 R G + + +L A+ + S P +P PP L+++ FGT + Sbjct: 42 RPGFSLALLIVLFALLCALAPHWLSSFDPYATAPADKLSPPSLAHW---FGTDELGRDLY 98 Query: 77 VQIIQGAKSVIEISFLAGLFATLIGIVVGIIAGYLGGIIDNILMGITDIILTLPSLILII 136 +++ GA+ + + LA A L G+ +G++AG+ GG +D LM + D++L LP L+L + Sbjct: 99 TRVVYGARLSVLAALLAVAIALLGGLGLGVLAGFAGGHVDAALMRLIDVLLALPGLLLAL 158 Query: 137 IIVSAFKTSNPIFLSLILSITSWAGLARAVRSQVLVIRNSPAVEVLRVLGLSRKYIIFRE 196 IV+A + +++ + + G AR R++VL I+ P VE R+ G S + R Sbjct: 159 AIVTAIGFGT-VPVAVAVGVGILPGFARTTRAEVLRIKTLPFVEAARLCGASWARTLLRH 217 Query: 197 VVPTLGSYIAIHYIFNVEAAVYAEVGLYYLGVLPYNP-NNWGAMI 240 V+P S +A+ + AA+ A GL +LG P WG +I Sbjct: 218 VLPNAWSPVAVLATLDFGAAILATAGLSFLGFGAAPPAAEWGTLI 262 Lambda K H 0.328 0.146 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: 189 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: 290 Length of database: 302 Length adjustment: 26 Effective length of query: 264 Effective length of database: 276 Effective search space: 72864 Effective search space used: 72864 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: 48 (23.1 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