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 BPHYT_RS17465 BPHYT_RS17465 glycerol-3-phosphate transporter membrane protein
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__BFirm:BPHYT_RS17465 Length = 281 Score = 139 bits (350), Expect = 7e-38 Identities = 85/272 (31%), Positives = 137/272 (50%), Gaps = 16/272 (5%) Query: 8 HAGPVTYVVLTVFALVSLAPLVWTAIAASRTNHRLAETPPPLWFGGNLFKNLEAAWEQ-- 65 HA + VVL VF P+ AA+ + H + P L +L +N+ W Q Sbjct: 13 HAVLILGVVLVVF------PVYVAFCAATMSEHEVFSVPLSLVPSTHLLENIATVWSQGS 66 Query: 66 ----AGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQ 121 A G + NS+++A I++ + S ++ +A RF F L L T+M+P + Sbjct: 67 GNAAAPFGRMLFNSLVMALVISIGKIAVSMISAYAIVFFRFPFRNLAFWLIFITLMLPVE 126 Query: 122 LAVVPLYLWMSDLGWSNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSL 181 + + P +S + SN + LP + +A TF RQ+ + LP EL+EAAR+DGA ++ Sbjct: 127 VRIFPTVQVVSSMHLSNTYSGLTLPLIASATATFLFRQFFM-TLPDELMEAARIDGAGAM 185 Query: 182 RIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQNPT---VQVGPELARHRVLP 238 R W VV P ++ MA L ++TF++ WN +LWPI+ +QQ+ T V + +A Sbjct: 186 RFFWDVVLPLSKTNMAALFVITFIYGWNQYLWPILITSQQSLTTAVVGIKSMIASGDTAT 245 Query: 239 DQAVIMAGALLGTLPLLVAFLLFGKQIVGGIM 270 + ++M LL LP L L + V G++ Sbjct: 246 EWHLVMTATLLAMLPPLAVVLTMQRWFVRGLV 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: 241 Number of extensions: 16 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: 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