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 HSERO_RS22225 HSERO_RS22225 ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS22225 Length = 325 Score = 400 bits (1029), Expect = e-116 Identities = 207/327 (63%), Positives = 257/327 (78%), Gaps = 4/327 (1%) Query: 7 LALGVALAVAMMAGTASAKDIKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGPT 66 LA G A+ + A +A+ ++I +VVKSLGNGFFDAA++GA+EAA+ELG VEVIYTGPT Sbjct: 1 LAAG-AIGLIAAAPAHAAEKVRIAMVVKSLGNGFFDAAHEGAKEAARELGDVEVIYTGPT 59 Query: 67 STTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRIL 126 + TAEGQIE++NSLI+Q VDAI +SAND +ALVP K+A QRG+KV+S+DSG+A GR++ Sbjct: 60 TPTAEGQIEIVNSLISQKVDAIVISANDANALVPITKRAMQRGVKVLSFDSGIAKGGRLM 119 Query: 127 QLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLK--DFPGL 184 QLNPS+ ELIG + +A + + GG GD AILSAT +TNQNIWI +MKK L +F + Sbjct: 120 QLNPSNAELIGLKQIQMAAEAI-GGAGDVAILSATAQATNQNIWIGEMKKALARPEFSRM 178 Query: 185 NLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVTG 244 LV TVYGDD SDKSYREA GLL+S+P +K I+APTTVG+ AA K V D+ LVGKVYVTG Sbjct: 179 KLVATVYGDDQSDKSYREAIGLLRSHPGLKAIIAPTTVGINAAGKAVVDEKLVGKVYVTG 238 Query: 245 LGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKIK 304 LGLPSEMAG +KSGA K FAIWNPIDLGY+AT AY+ VKG+ GK G I GRMG IK Sbjct: 239 LGLPSEMAGHVKSGAVKSFAIWNPIDLGYAATYAAYQFVKGKAQGKEGESIAVGRMGSIK 298 Query: 305 VGDNGEAAMADPFVYNASNIDQFSKVF 331 + GEAA+A PF Y+ASN+D+F+K+F Sbjct: 299 LDAAGEAALAPPFTYDASNVDKFAKIF 325 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: 356 Number of extensions: 8 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: 325 Length adjustment: 28 Effective length of query: 303 Effective length of database: 297 Effective search space: 89991 Effective search space used: 89991 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