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 SM_b20484 SM_b20484 sugar ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Smeli:SM_b20484 Length = 330 Score = 129 bits (325), Expect = 8e-35 Identities = 102/297 (34%), Positives = 156/297 (52%), Gaps = 12/297 (4%) Query: 3 LAKTLALGVALAVAMMAGTASAKDI-KIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVI 61 LA LA ++LA A TA+A+D K+G+VVK G +F+A G +E ++LG V+ Sbjct: 6 LAAALAASLSLAGAY---TAAAQDTGKVGVVVKIGGIPWFNAMEAGIKERGEKLG-VDAF 61 Query: 62 YTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAP 121 GPTS Q+ I LIAQ V I V ND L P L KA ++GI VI+ +S + Sbjct: 62 MVGPTSADPALQVRAIEDLIAQNVKVIGVVPNDAKVLEPVLTKAREKGIIVITHESP-SQ 120 Query: 122 EGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK-D 180 +G +S G+ L + + GGKG++A+ + T N W D + +K + Sbjct: 121 KGADWDFELASATGFGEAHAKLLAEKM-GGKGEYAVFVGSLTVPLHNAWADAAIEYIKKN 179 Query: 181 FPGLNLVTTVYG--DDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVG 238 P + LV YG +D+ DKS A L+ ++P++K +A + G + A + +E++ VG Sbjct: 180 HPEMTLVGDRYGVAEDV-DKSRSTALDLISAHPDLKGFLAFGSQGPIGAGRAIEERRKVG 238 Query: 239 KVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEI 295 +++V G P + IKS A +WNP G +A +L+KGE + K G EI Sbjct: 239 EIFVLGPFSPGQGQKLIKSDAISGGFMWNPKQAGEVFVTLAAKLMKGE-EIKDGEEI 294 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: 287 Number of extensions: 19 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: 331 Length of database: 330 Length adjustment: 28 Effective length of query: 303 Effective length of database: 302 Effective search space: 91506 Effective search space used: 91506 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