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 3609045 Dshi_2434 rhamnose ABC transporter, periplasmic rhamnose-binding protein (RefSeq)
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Dino:3609045 Length = 333 Score = 441 bits (1135), Expect = e-129 Identities = 223/326 (68%), Positives = 270/326 (82%), Gaps = 2/326 (0%) Query: 7 LALGVALAVAMMAGTASAKD-IKIGLVVKSLGNGFFDAANKGAQEAAKELGGVEVIYTGP 65 L G++LA ++ TA A+D ++I LVVK+LG GFF+AA +GA+EAA ELGGVE+IYTGP Sbjct: 9 LTAGLSLAASLFGTTAMAQDEMRIALVVKALGIGFFEAAAQGAEEAAAELGGVEIIYTGP 68 Query: 66 TSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDSGVAPEGRI 125 T TTAEGQIEVINSLIAQGVDAIAVSAND DALVP LKKA QRGI VISWDSGVAPEGR Sbjct: 69 TDTTAEGQIEVINSLIAQGVDAIAVSANDTDALVPTLKKAMQRGITVISWDSGVAPEGRQ 128 Query: 126 LQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQLKDFPGLN 185 + LNPSSN LIG M + LA DHL G GD A+LSATTTSTNQNIWI++M K L D+PG+N Sbjct: 129 MHLNPSSNALIGNMIIKLAADHLPDG-GDVAVLSATTTSTNQNIWIEEMTKVLGDYPGIN 187 Query: 186 LVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGLVGKVYVTGL 245 +V+TVYGDDL+DKSYREA+GL++S P++ I+APT+VG++AA++ V D G +G+V VTGL Sbjct: 188 VVSTVYGDDLADKSYREAQGLMQSFPDLDAIIAPTSVGIVAAAQAVADAGKIGQVNVTGL 247 Query: 246 GLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEINAGRMGKIKV 305 GLPSEMAGAI+SGA+K FAIWNPIDLGYSA IA+ L G +PG+EI+ GR+G I + Sbjct: 248 GLPSEMAGAIESGASKSFAIWNPIDLGYSAAMIAHALASGAATAEPGTEISIGRVGTITL 307 Query: 306 GDNGEAAMADPFVYNASNIDQFSKVF 331 +N EAAMADPF+Y+ASNIDQF +F Sbjct: 308 DENNEAAMADPFIYDASNIDQFKSIF 333 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: 385 Number of extensions: 12 Number of successful extensions: 2 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: 333 Length adjustment: 28 Effective length of query: 303 Effective length of database: 305 Effective search space: 92415 Effective search space used: 92415 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