Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 172 bits (436), Expect = 1e-47 Identities = 114/326 (34%), Positives = 174/326 (53%), Gaps = 20/326 (6%) Query: 17 ARRSSSTTAQW-LLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAI 75 A ++ +A W LH LG PV+ ++ L G L SNFA+ +N MN+L + A Sbjct: 25 AAAATGASAWWGKLHGLG--PVIGLVLLCIAGTLL------NSNFATYDNVMNVLTRTAF 76 Query: 76 NLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMF---------IFS 126 ++A GM FVI++ GIDLSVGS+ A+ A + AP PM + Sbjct: 77 IGIIAVGMCFVIISGGIDLSVGSMAALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVL 136 Query: 127 GLVMGMVNGAMVALLNINAFVVTLGTMTAFRG-AAYLLADGTTVLNNDIPS-FEWIGNGD 184 G V G+V+G ++ I F+VTLGT+ FR Y G L ND+ + + + Sbjct: 137 GAVFGLVHGLLITKGRIEPFIVTLGTLGIFRAYLTYFSNGGAITLENDLSDIYSPVYYAN 196 Query: 185 FLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISG 244 L VP +W+ + V ++ VIL +T G ++ AIG N Q A+ + V + + Y + G Sbjct: 197 LLGVPIPVWIFLLVAIVGGVILNRTAYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLG 256 Query: 245 LFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVM 304 + G+A + RL A+ G +EL+AIAAV++GGT L GG GSI GTVVGA+++ V+ Sbjct: 257 VCVGIATLLYVPRLGSASPTTGLLWELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVI 316 Query: 305 NNGLTILGLSSFWQYVAKGAVIVLAV 330 +N L + + S + A +++AV Sbjct: 317 SNILNLTSIISVYLNAAVQGFVIIAV 342 Lambda K H 0.324 0.138 0.417 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: 363 Number of extensions: 29 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: 344 Length of database: 350 Length adjustment: 29 Effective length of query: 315 Effective length of database: 321 Effective search space: 101115 Effective search space used: 101115 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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