Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 212 bits (540), Expect = 1e-59 Identities = 140/339 (41%), Positives = 187/339 (55%), Gaps = 28/339 (8%) Query: 17 PAGTLGRLTTQER---LRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLA 73 P L R Q R ++ L LV+L + FS+ + F NL +A Q + L Sbjct: 8 PNQALDRQVQQRRRDLIQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQVTSIAYLG 67 Query: 74 AGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGI----VNG 129 T VI+TGGIDLSVGS+L+++ V A +L+ + G+ +P A+L G+L G VNG Sbjct: 68 VAATCVIITGGIDLSVGSVLALAGVAA---ALLVKAGV-PIPVAMLGGMLVGAACGWVNG 123 Query: 130 ALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVL---------- 179 V M LPPFI TLG + RGLA + + F +GNG + Sbjct: 124 ICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFRISHIGADGF 183 Query: 180 ------GVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVY 233 G+P+ V+I + A +L RT LG IYAVG NAEAARLSG+ V V LF Y Sbjct: 184 PDTVFPGIPYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTY 243 Query: 234 AVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGAL 293 +SGLLAG G + +RL A + G YELDAIA+ ++GGTS +GG G+I GT +GA Sbjct: 244 VLSGLLAGATGCVLMSRLVTAQPNE-GVMYELDAIASAVIGGTSLMGGVGTISGTAIGAF 302 Query: 294 IIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 +I VL NGL + GVS Q II G+VI+G V +D R + Sbjct: 303 VIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQLRNR 341 Lambda K H 0.325 0.141 0.409 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: 399 Number of extensions: 23 Number of successful extensions: 4 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: 337 Length of database: 343 Length adjustment: 28 Effective length of query: 309 Effective length of database: 315 Effective search space: 97335 Effective search space used: 97335 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