Align Ribose import permease protein RbsC (characterized)
to candidate WP_061940318.1 CPter91_RS11535 ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >NCBI__GCF_001584185.1:WP_061940318.1 Length = 334 Score = 202 bits (515), Expect = 7e-57 Identities = 114/301 (37%), Positives = 177/301 (58%), Gaps = 10/301 (3%) Query: 23 LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 ++ L+ L + L+ +F T++NL N+L +T+ I+AVGMT VI++ GIDLSVGS+ AL Sbjct: 27 VLGLIGLCIAGTLLNGDFATVDNLMNVLTRTAFIGIIAVGMTFVIISGGIDLSVGSMAAL 86 Query: 83 TGA---------VAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVM 133 ++A +G L+ +A AL LG A G + G+++ KG+++AFI TL Sbjct: 87 IAGSMIYFMNMLMSAGTLGPLTILLIGIAMALLLGLAFGCLHGLLITKGKIEAFIVTLGT 146 Query: 134 MLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHT 193 + + R V +G + + +DL+ LG+P P+W+ V L +L+ T Sbjct: 147 LGIFRSVLTYLADGGALTLD-NQLSDLYSPVYYTSLLGIPIPIWVFLAVALGGALILNRT 205 Query: 194 RLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGY 253 GR++ A+G NE R + I V+ +K Y L G+ +A ++ V RL SA PT G + Sbjct: 206 AFGRHVQAIGSNEQVARYAAIRVDFVKTCTYMLLGVCVGIATVLYVPRLGSASPTTGLLW 265 Query: 254 ELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLA 313 EL+AIAAVV+GGT+L GG GRIVGT++GA++L ++N LNL + S Y V+++A Sbjct: 266 ELEAIAAVVVGGTALKGGSGRIVGTVVGAILLSVISNILNLTSIISVYLNAAVQGVVIIA 325 Query: 314 V 314 V Sbjct: 326 V 326 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: 261 Number of extensions: 10 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: 321 Length of database: 334 Length adjustment: 28 Effective length of query: 293 Effective length of database: 306 Effective search space: 89658 Effective search space used: 89658 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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