Align RhaP, 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 YP_004141943.1 Mesci_2759 inner-membrane translocator
Query= TCDB::Q7BSH3 (333 letters) >NCBI__GCF_000185905.1:YP_004141943.1 Length = 338 Score = 189 bits (481), Expect = 7e-53 Identities = 115/319 (36%), Positives = 177/319 (55%), Gaps = 18/319 (5%) Query: 2 ARLIRKRETLLFLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKS 61 ARL+ LLFL V +I+VF+ F P NL I SI ++AL VILT Sbjct: 16 ARLLMSFGPLLFL--VALIIVFTVLKPSFMDPINLFNITRQISITGLIALGMTFVILTAG 73 Query: 62 IDLSVAANLAFTGMAIAMM------------NAAHPDLPLVVLILMAVVIGACLGAINGF 109 IDLSV + LAF GM A++ + +L A+++GA G + G Sbjct: 74 IDLSVGSLLAFCGMVAAVVAKGGTANTLSLSTSGTQGFGWFAALLAAIIVGAAAGGVQGL 133 Query: 110 LVWALEIPPIVVTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLG-LPVLSWV 168 ++ L++PP VVTLG LT++RG+ +S G ++ + + T ++G +PV + + Sbjct: 134 VITRLKVPPFVVTLGGLTVFRGLTLTISNGGPISGFDASMRWFG---TGLIGPVPVPALI 190 Query: 169 GIIIVILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLW 228 IL +++LRYT++GR+ YA GGN AA +G+ +V+ G AGLA+++ Sbjct: 191 FAAAAILCHIVLRYTRYGRAVYAVGGNAEAARLSGLRVDRILVSVYVIVGFFAGLAAFVL 250 Query: 229 VSRYAVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGIS 288 +R + G+EL ++A VIGG S+ GG+GSV GTV+GA +GV++N L +S Sbjct: 251 SARLNSSEAVAGIGYELTVISAVVIGGTSLFGGIGSVGGTVVGAALIGVLQNGLQFNNVS 310 Query: 289 PFTQMAISGTVIILAVAFN 307 +TQ + G ++ILAVAF+ Sbjct: 311 SYTQSIVIGLILILAVAFD 329 Lambda K H 0.328 0.141 0.413 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: 299 Number of extensions: 18 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: 333 Length of database: 338 Length adjustment: 28 Effective length of query: 305 Effective length of database: 310 Effective search space: 94550 Effective search space used: 94550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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