Align Ribose import permease protein RbsC (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 237 bits (605), Expect = 3e-67 Identities = 135/313 (43%), Positives = 199/313 (63%), Gaps = 5/313 (1%) Query: 10 RYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILT 69 R F A + + +LL++I S SPNF ++NL +ILQ T+VN ++A+ T VI+T Sbjct: 27 RLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIIT 86 Query: 70 SGIDLSVGSLLALTGAVAASIVGIEVNAL-VAVAAALALGAAIGAVTGVIVAKGRVQAFI 128 SGIDLSVG+++ +A ++ L + +AAA+ GA G ++G+++AK +V FI Sbjct: 87 SGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFI 146 Query: 129 ATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFG-IGR---PLGVPTPVWIMGIVFL 184 ATL MM+LL+G+++V + P+ TE IG L +P V I+ +V + Sbjct: 147 ATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAI 206 Query: 185 AAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSS 244 A +L+ T GRY +ALG NE A RLSG+ V+ K+ VY+ G + +AG+I +RL+S Sbjct: 207 GASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNS 266 Query: 245 AQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMI 304 AQP G GYELDAIAAVV+GGTSL+GG G I+GT+IGA I+ L NGL ++ V+ +Q + Sbjct: 267 AQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTV 326 Query: 305 VKAVVILLAVLVD 317 V V+I+LAV +D Sbjct: 327 VTGVIIILAVYLD 339 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: 245 Number of extensions: 11 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: 347 Length adjustment: 28 Effective length of query: 293 Effective length of database: 319 Effective search space: 93467 Effective search space used: 93467 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