Align RhaP, 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 3607107 Dshi_0529 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Dino:3607107 Length = 333 Score = 157 bits (397), Expect = 4e-43 Identities = 99/317 (31%), Positives = 166/317 (52%), Gaps = 13/317 (4%) Query: 7 KRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSV 66 + ETL+ +I++ V + F T ++ + + ++ ILA+ M V+++ ID+S Sbjct: 12 RNETLVAGVIMLFCFVATVSDPRFLTITTVSDLLRASIVIGILAVGAMLVLVSGGIDVSF 71 Query: 67 AANLAFTGMAIAMMNAA-HPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGT 125 A F + +++ P++P V+ +++VV GA LGAINGF + L +P ++VTLGT Sbjct: 72 TAIAVFAMYSSTVLSLTIWPEIPWPVIFVISVVFGAALGAINGFFIAFLGLPTLIVTLGT 131 Query: 126 LTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPV----------LGLPVLSWVGIIIVIL 175 L+I+RG G ++ + P R + +P + + +++L Sbjct: 132 LSIFRGFLLTFIGSQRIS--DLPPSMRDFSRGVIARGTTEAGNFYSIPWAALALLFVIVL 189 Query: 176 MYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVA 235 + +L+ T GRS YA GG+ +A GI+ WT+F +V GALAGLA + S +A Sbjct: 190 TWFILKKTMLGRSIYAIGGSVESARRIGINVKWTQFFVYVYVGALAGLAGIIHGSVGRMA 249 Query: 236 YVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAI 295 G EL +AA V+GG + GG G++ GT+LG + +++N+L VIGI Q Sbjct: 250 DPFSLVGLELSVIAAVVLGGARLIGGYGTLTGTMLGVALIVIVQNSLIVIGIPTTWQSVT 309 Query: 296 SGTVIILAVAFNARRER 312 G +I+L A R + Sbjct: 310 IGILILLGTGVPAYRAK 326 Lambda K H 0.328 0.141 0.413 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: 309 Number of extensions: 14 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: 333 Length of database: 333 Length adjustment: 28 Effective length of query: 305 Effective length of database: 305 Effective search space: 93025 Effective search space used: 93025 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 (21.8 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