Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate 208684 DVU3164 ABC transporter, permease protein
Query= TCDB::Q9X9R5 (276 letters) >MicrobesOnline__882:208684 Length = 277 Score = 140 bits (353), Expect = 3e-38 Identities = 87/261 (33%), Positives = 135/261 (51%), Gaps = 9/261 (3%) Query: 17 LTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQAGLGTAMLNSV 76 L + + L +WTA S + R P +N AW A +N+V Sbjct: 24 LAIMWALPLLYAIWTAFHPSAYSTRFTLNAPLT------LENFVTAWHAAPFALYFVNTV 77 Query: 77 IVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWMSDLGW 136 ++ + + ++ TLA +AFAK FR ++ L + +MI P + VV Y M+ +G Sbjct: 78 LLVTMVLAAQLVLCTLAAYAFAKYDFRGKNIMFALVLMQLMIMPDVLVVENYRTMASIGV 137 Query: 137 SNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFPAARPAM 196 + + LP + +AFG F +RQ +++P EL EAA V+GAS+L+I+W V P +P Sbjct: 138 LDSTLAIGLPYMASAFGIFLLRQTF-KSIPKELDEAAAVEGASTLQILWKVYVPLGKPVY 196 Query: 197 AVLGLLTFVFAWNDFLWPIIALNQQNP-TVQVGPEL-ARHRVLPDQAVIMAGALLGTLPL 254 L++ + WN+FLWP+I N N + VG ++ + D A+I A L+ + PL Sbjct: 197 LAYALVSISYHWNNFLWPLIVTNTTNSRPLTVGLQVFSSTEQGVDWAIITAATLMTSGPL 256 Query: 255 LVAFLLFGKQIVGGIMQGAIK 275 LVAFLLF +Q V M+ IK Sbjct: 257 LVAFLLFQRQFVQSFMRAGIK 277 Lambda K H 0.327 0.140 0.434 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: 213 Number of extensions: 11 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 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: 47 (22.7 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