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 GFF3640 PGA1_262p00440 xylose transport system permease protein XylH
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Phaeo:GFF3640 Length = 433 Score = 95.1 bits (235), Expect = 3e-24 Identities = 52/144 (36%), Positives = 84/144 (58%) Query: 161 GLPVLSWVGIIIVILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGAL 220 GLP+ + I ++M ++ R T+ GR +ATGGNP AA +GI+T F L G L Sbjct: 276 GLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAELSGINTRLLTVKIFALMGFL 335 Query: 221 AGLASYLWVSRYAVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKN 280 L++ + +R A DI EL +AA VIGG +++GG G++ G +LGAL + +++ Sbjct: 336 CALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQS 395 Query: 281 ALPVIGISPFTQMAISGTVIILAV 304 + ++G+ Q + GTV++ AV Sbjct: 396 GMAMVGVDAPFQNIVVGTVLVAAV 419 Score = 66.6 bits (161), Expect = 1e-15 Identities = 55/187 (29%), Positives = 87/187 (46%), Gaps = 15/187 (8%) Query: 30 FATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFTGMAIAMMNA-AHPDL- 87 F TP N+ + T + I+A + VI+T+ IDLSV A LA +A++ PD+ Sbjct: 49 FLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMF 108 Query: 88 --------PLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAFVLSGG 139 ++ + + + IG +GA G++V L IP +VTLG ++R +A+ L+ G Sbjct: 109 GLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDG 168 Query: 140 AWVNAHQMTPIFLSVPRTPVLGLPVLSW-VGIIIVILMYVLLRYTQFGRSAYATGGNP-- 196 + T FL T LSW VGI+ +L L ++ + + P Sbjct: 169 QTIGPLDST--FLVFGGTSGTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAW 226 Query: 197 TAAVYAG 203 AV AG Sbjct: 227 AEAVIAG 233 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: 335 Number of extensions: 23 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 333 Length of database: 433 Length adjustment: 30 Effective length of query: 303 Effective length of database: 403 Effective search space: 122109 Effective search space used: 122109 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: 50 (23.9 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