Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 217 bits (552), Expect = 3e-61 Identities = 118/316 (37%), Positives = 194/316 (61%), Gaps = 1/316 (0%) Query: 9 PVTAAPRNRLRLSLDRF-GLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVG 67 P T A L LS+ + G V +LL + + + F++ N ++I Q++I ++A+ Sbjct: 2 PDTNALPRPLGLSIGKVPGSVWVLLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALP 61 Query: 68 MTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANL 127 MT +I+T+G+DLS+G++L G+ AMV L A+ A + G G++NG +V+ L Sbjct: 62 MTLIIMTEGLDLSMGAVLTLCGVVLAMVMVATESLPLALGAALLTGLAFGLLNGALVSWL 121 Query: 128 SIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIF 187 IPPFVATLG L +A+G+ + DG +T + +A + G++ + +PI I AV +F Sbjct: 122 EIPPFVATLGTLGVAQGLALVATDGQSVTGIGEAIPLIYAGQLLGVPLPIWIAAVFYGLF 181 Query: 188 WMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSAL 247 +L +T +G YV+A+GGN ++ + SG+ + + +VY + GL+AG+A ++L+AR + Sbjct: 182 HWLLYHTRFGAYVFALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGH 241 Query: 248 PQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAK 307 P A + E DAIAAV +GGT+ G G + GT+ G L +GV+ NGLNL+GV S Q A Sbjct: 242 PTAAIGLEFDAIAAVAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAI 301 Query: 308 GLIIVFAVLIDVWRKK 323 GL+++ +LI+ ++ K Sbjct: 302 GLLVLVVLLIESFKGK 317 Lambda K H 0.326 0.141 0.412 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: 277 Number of extensions: 17 Number of successful extensions: 1 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: 325 Length of database: 318 Length adjustment: 28 Effective length of query: 297 Effective length of database: 290 Effective search space: 86130 Effective search space used: 86130 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 (21.6 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