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 BWI76_RS26295 BWI76_RS26295 glycerol-3-phosphate transporter membrane protein
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__Koxy:BWI76_RS26295 Length = 281 Score = 121 bits (304), Expect = 1e-32 Identities = 79/267 (29%), Positives = 133/267 (49%), Gaps = 10/267 (3%) Query: 13 TYVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAW------EQA 66 ++ +L + V L PL +AA+ + + +TP L GG+L +N++ W A Sbjct: 12 SHTMLILGIAVILFPLYVAFVAATLDSKAVFDTPMTLIPGGHLLENMKFIWVNGVGANSA 71 Query: 67 GLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVP 126 MLNS I+A ITV + S L+ FA RF L + T+M+P ++ + P Sbjct: 72 PFWLMMLNSFIMAFGITVGKITVSMLSAFAIVWFRFPLRNLFFWMIFITLMLPVEVRIFP 131 Query: 127 LYLWMSDLGWSNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWH 186 +++L + + LP + +A TF RQ+ + LP ELIEAAR+DGAS +R Sbjct: 132 TVEVIANLKMLDSYAGLTLPLMASATATFLFRQFFM-TLPDELIEAARIDGASPMRFFRD 190 Query: 187 VVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQN---PTVQVGPELARHRVLPDQAVI 243 +V ++ +A L ++TF++ WN +LWP++ + N + +A + + Sbjct: 191 IVLQLSKTNLAALFVITFIYGWNQYLWPLLIITDVNLGTAVAGIKGMIAIGQGTTQWNQV 250 Query: 244 MAGALLGTLPLLVAFLLFGKQIVGGIM 270 MA LL +P +V L + V G++ Sbjct: 251 MAAMLLTLIPPVVIVLAMQRAFVRGLV 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: 244 Number of extensions: 13 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: 281 Length adjustment: 25 Effective length of query: 251 Effective length of database: 256 Effective search space: 64256 Effective search space used: 64256 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