Align RhaS, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BWI76_RS00665 BWI76_RS00665 rhamnose ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Koxy:BWI76_RS00665 Length = 328 Score = 427 bits (1097), Expect = e-124 Identities = 220/327 (67%), Positives = 270/327 (82%), Gaps = 7/327 (2%) Query: 8 ALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGPTS 67 +L + +A+ ++G+A A ++KI LV KSLGNGFF+AAN GAQEAAKELG V+VIYTGPT+ Sbjct: 6 SLILTVAILALSGSALA-EVKIALVAKSLGNGFFEAANVGAQEAAKELGDVKVIYTGPTT 64 Query: 68 TTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRILQ 127 TTAE QIEV+N LIAQGVDAIA+SANDPDA+VP LKKA QRGIKV+SWDSGVAP GR + Sbjct: 65 TTAEAQIEVLNGLIAQGVDAIAISANDPDAVVPVLKKAMQRGIKVVSWDSGVAPAGRQIH 124 Query: 128 LNPSSNELIGKMCLTLAKDHLEG---GKGDFAILSATTTSTNQNIWIDQMKKQLKDFPGL 184 LNPS+N LIG+ + LA D L+ KGD AILSAT TSTNQNIWI++MKK L +P + Sbjct: 125 LNPSNNALIGETNVKLAADALKALNVEKGDVAILSATPTSTNQNIWIEEMKKVLPQYPSV 184 Query: 185 NLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVTG 244 NLVT YGDDLSDKSYREA GLLKS P++KVIV+P++VG++AA++ V+D+G +GKVYVTG Sbjct: 185 NLVTVAYGDDLSDKSYREAVGLLKSYPDLKVIVSPSSVGIVAAAQAVKDQGKIGKVYVTG 244 Query: 245 LGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKIK 304 LGLPSEMAGAIKSGA+K FAIWNPIDLGY+AT +A LVKG +E N G++GK+K Sbjct: 245 LGLPSEMAGAIKSGASKSFAIWNPIDLGYAATYLADDLVKGTA---TKTEANMGKLGKVK 301 Query: 305 VGDNGEAAMADPFVYNASNIDQFSKVF 331 + +G AMA+PFVY+ASNID+FSK+F Sbjct: 302 LDADGSGAMAEPFVYDASNIDKFSKIF 328 Lambda K H 0.313 0.131 0.365 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: 411 Number of extensions: 12 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: 331 Length of database: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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