Align Ribose import permease protein RbsC (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 219 bits (558), Expect = 7e-62 Identities = 124/295 (42%), Positives = 187/295 (63%), Gaps = 4/295 (1%) Query: 23 LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 L AL +L +++ S F T+ N+ N+L+Q S+ ++A G+TLVILT G+DLSVG+ +A+ Sbjct: 21 LFALGLLCLLLAVASDAFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVAM 80 Query: 83 TGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTM 142 + VAA+++ + ++ V A L GA IG G++VA R+ FIAT M+ +L GVT Sbjct: 81 SACVAATVMKATGSTMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVLHGVTY 140 Query: 143 VYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYAL 202 + G ++ GF F G G GVP PV++M + +A M T G+ IYA+ Sbjct: 141 WFMAGETIH-GFPP---AFRAIGSGYLWGVPIPVYLMLVFLVAGTAMSQKTTYGQEIYAI 196 Query: 203 GGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVV 262 G N A RLSG+ V + ++VY + G +A +A ++ +ARL+SA+ G L AIAAV+ Sbjct: 197 GANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDIGEALTLPAIAAVL 256 Query: 263 LGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 +GGTSL GG GR+ GTL+GA+IL + NG+NLL VS+ +Q +V V+++LAV +D Sbjct: 257 IGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVIVVLAVFLD 311 Lambda K H 0.324 0.139 0.393 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: 265 Number of extensions: 14 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: 321 Length of database: 322 Length adjustment: 28 Effective length of query: 293 Effective length of database: 294 Effective search space: 86142 Effective search space used: 86142 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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