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_b21016 SM_b21016 sugar ABC transporter substrate-binding protein
Query= TCDB::Q7BSH5 (331 letters) >FitnessBrowser__Smeli:SM_b21016 Length = 343 Score = 172 bits (435), Expect = 1e-47 Identities = 100/312 (32%), Positives = 172/312 (55%), Gaps = 8/312 (2%) Query: 3 LAKTLALGVALAVAMMAGTASAK-----DIKIGLVVKSLGNGFFDAANKGAQEAAKELGG 57 + KT+ ALA A++AGT A + +I + K +G GFF + GA +A +E+G Sbjct: 1 MIKTIMKSSALAAALLAGTVLASGAAHAENQIAFIPKLVGVGFFTSGGAGAVKAGEEVGA 60 Query: 58 VEVIYTGPTSTTAEGQIEVINSLIAQGVDAIAVSANDPDALVPALKKATQRGIKVISWDS 117 +V Y GPT + GQ++ IN+ + QG +A+ VS+ PD L PALK+A +RG+ V++WDS Sbjct: 61 -KVTYDGPTEPSVSGQVQFINNFVNQGYNALIVSSVSPDGLCPALKRAMERGVLVMTWDS 119 Query: 118 GVAPEGRILQLNPSSNELIGKMCLTLAKDHLEGGKGDFAILSATTTSTNQNIWIDQMKKQ 177 V P+ R +N + E +G + + +A + ++ K A ++ T T+QN W + K + Sbjct: 120 DVNPDCRSYYINQGTPEQLGGLLVDMAAEGVKKEKAKVAFFYSSPTVTDQNAWAEAAKAK 179 Query: 178 L-KDFPGLNLVTTVYGDDLSDKSYREAEGLLKSNPNVKVIVAPTTVGVLAASKVVEDKGL 236 + K+ PG +VTT YG + + KS + AE +L++ P++ I+AP + AA++ E+ Sbjct: 180 IAKEHPGWEIVTTQYGYNDAQKSLQTAESILQTYPDLDAIIAPDANALPAAAQAAENLKR 239 Query: 237 VGKVYVTGLGLPSEMAGAIKSGATKEFAIWNPIDLGYSATQIAYRLVKGETDGKPGSEIN 296 V + G P+ M I+ G + F +W+ G + +A ++K K G ++ Sbjct: 240 AEGVTIVGFSTPNVMRPYIERGTIQRFGLWDVTQQGKISVFVADHVLK-NGPMKVGEKLE 298 Query: 297 AGRMGKIKVGDN 308 +G ++V N Sbjct: 299 IPGVGTVEVSAN 310 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: 263 Number of extensions: 8 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: 343 Length adjustment: 28 Effective length of query: 303 Effective length of database: 315 Effective search space: 95445 Effective search space used: 95445 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