Align RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate H281DRAFT_01220 H281DRAFT_01220 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_01220 Length = 335 Score = 258 bits (660), Expect = 1e-73 Identities = 144/325 (44%), Positives = 206/325 (63%), Gaps = 6/325 (1%) Query: 8 ALGVAL-AVAMMAGTASAKD-IKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGP 65 AL VAL A++ A A K+ +KI V K + N + A+ G A KE GGV + GP Sbjct: 12 ALCVALLAISCAASAAGLKNGLKIAFVPKQINNPYEVIADDGGLAAIKEFGGVGKV-VGP 70 Query: 66 TSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRI 125 + A Q++ IN+LI Q DAI ++AND +A+VP LKKA +GIKV+++DS APEGR Sbjct: 71 SDAGASSQVQYINTLITQRQDAIVIAANDANAVVPYLKKAMSQGIKVVTFDSDTAPEGRQ 130 Query: 126 LQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK--DFPG 183 L +N ++ E IG+ + L L GG+G+FA+LSAT +TNQN WI M+++LK ++ Sbjct: 131 LFVNQANAEGIGRGQIQLVSK-LMGGEGEFAVLSATPNATNQNTWIKWMQEELKKPEYSK 189 Query: 184 LNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVT 243 + LV YG+D KS+ E +GLL++ PN+K IVAPTTVG+ AA++ + GKV VT Sbjct: 190 IKLVKIAYGNDDDQKSFVETQGLLQAYPNLKAIVAPTTVGIAAAARYISSSSSKGKVAVT 249 Query: 244 GLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKI 303 GLG P++M +K+G K F +W+P +LGY A A L G +GK G +AG++GK Sbjct: 250 GLGTPNQMRAFVKNGTVKAFQLWDPNELGYLAGYAAAALASGTINGKEGESFDAGKLGKR 309 Query: 304 KVGDNGEAAMADPFVYNASNIDQFS 328 +G GE + P ++ASNID+F+ Sbjct: 310 TIGPQGEIILGPPTTFDASNIDKFN 334 Lambda K H 0.313 0.131 0.365 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: 329 Number of extensions: 15 Number of successful extensions: 4 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: 331 Length of database: 335 Length adjustment: 28 Effective length of query: 303 Effective length of database: 307 Effective search space: 93021 Effective search space used: 93021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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