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 SMc02772 SMc02772 sugar ABC transporter permease
Query= TCDB::Q7BSH3 (333 letters) >FitnessBrowser__Smeli:SMc02772 Length = 324 Score = 187 bits (476), Expect = 2e-52 Identities = 108/304 (35%), Positives = 174/304 (57%), Gaps = 7/304 (2%) Query: 10 TLLFLIIVVMIVV-FSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAA 68 TL+ L++V+ +++ +T A F TP N++ + ++ ILA+ Q VI+T IDLSV A Sbjct: 24 TLVGLLVVLWLLLGLATNA--FWTPNNISNLLRQGAMTAILAVGQTFVIITAGIDLSVGA 81 Query: 69 NLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTI 128 + FT + +A + AA +PL + I+ + IG +GA + F + + +PP ++TL TLT Sbjct: 82 VVGFTSVIVAWLLAA--GVPLWLAIIATLAIGVLIGAFHAFGIVRMGLPPFIITLATLTS 139 Query: 129 YRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRS 188 RG+ +++ G+ ++ F + R LG+P L W+ I++ I YV L ++FGR Sbjct: 140 LRGIGLLITNGSTISI--TNDAFTTFSRADFLGIPSLFWMVIVVAIPAYVFLHLSRFGRY 197 Query: 189 AYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSV 248 +A G N AA +G++ T +LA++LS A L SR + A G+EL ++ Sbjct: 198 LFAVGSNSEAARLSGVNVNRTIYLAYILSSTCAAFVGLLLASRIGIGNATQAEGWELQAI 257 Query: 249 AACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNA 308 A+ VIGG S+ G VGSV G +LGA L I N ++ ++ F Q I+G +II+ V F+ Sbjct: 258 ASSVIGGTSLFGAVGSVHGPLLGAFILATINNGANLLNVNSFWQRIITGLLIIVIVYFDQ 317 Query: 309 RRER 312 R R Sbjct: 318 LRRR 321 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: 249 Number of extensions: 15 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: 333 Length of database: 324 Length adjustment: 28 Effective length of query: 305 Effective length of database: 296 Effective search space: 90280 Effective search space used: 90280 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