Align Ribose import permease protein RbsC (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 203 bits (516), Expect = 6e-57 Identities = 120/305 (39%), Positives = 183/305 (60%), Gaps = 11/305 (3%) Query: 27 LVLIAIVSTL-SPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL-TG 84 LVL+ I TL + NF T +N+ N+L +T+ I+AVGM VI++ GIDLSVGS+ AL G Sbjct: 47 LVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAALIAG 106 Query: 85 AVA------ASIVGIEVNALVA-VAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLL 137 +V A ++G + A+V + A+ LGA G V G+++ KGR++ FI TL + + Sbjct: 107 SVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLGIF 166 Query: 138 RGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGR 197 R ++NG + T + +D++ LGVP PVWI +V + +L+ T GR Sbjct: 167 RAYLTYFSNGGAI-TLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVILNRTAYGR 225 Query: 198 YIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDA 257 Y+ A+G NE + + ++V+KIKI+ Y L G+ +A ++ V RL SA PT G +EL+A Sbjct: 226 YVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLWELEA 285 Query: 258 IAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLG-VSSYYQMIVKAVVILLAVLV 316 IAAV++GGT L GG G I GT++GA++L ++N LNL +S Y V+ VI+ + Sbjct: 286 IAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIAVAFM 345 Query: 317 DNKKQ 321 K+ Sbjct: 346 QRGKR 350 Lambda K H 0.324 0.139 0.393 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: 273 Number of extensions: 12 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: 1 Length of query: 321 Length of database: 350 Length adjustment: 28 Effective length of query: 293 Effective length of database: 322 Effective search space: 94346 Effective search space used: 94346 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