Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_061946568.1 CPter91_RS23415 ABC transporter permease
Query= uniprot:D8IUD2 (328 letters) >NCBI__GCF_001584185.1:WP_061946568.1 Length = 333 Score = 509 bits (1312), Expect = e-149 Identities = 261/324 (80%), Positives = 295/324 (91%), Gaps = 3/324 (0%) Query: 5 SSTPAASRQAAY---LAGFKNYLGLMAALLAMCVMFAFLSENFLSAATFITLSNDIPPLV 61 SS+ +SR +++ ++G KNYLGL+ ALLAMC +F+ LSENFL+AATF TLSNDIP LV Sbjct: 7 SSSRLSSRWSSFNGSISGLKNYLGLIGALLAMCALFSVLSENFLTAATFTTLSNDIPTLV 66 Query: 62 VMSVGMTFILIIGGIDLSVGSVMALAASMLSMAMVRWGWPLYAAAPLGVVVAALCGTLTG 121 VM+VGMTF+LIIGGIDLSVGSVMALAAS+LSMAMVRWGWPL+ A L ++VA+LCG +TG Sbjct: 67 VMAVGMTFVLIIGGIDLSVGSVMALAASVLSMAMVRWGWPLFTAGILAMLVASLCGMVTG 126 Query: 122 MVSVHWRIPSFIVSLGVLEIARGLAYQVTNSRTEYIGSAVDVISSPILFGMSPAFLSAIA 181 ++SV WRIPSFIVSLGVLE+ARGLAYQVTNSRTEYIGSAVD ISSPILFGMSPAF+SAI Sbjct: 127 LISVGWRIPSFIVSLGVLEMARGLAYQVTNSRTEYIGSAVDGISSPILFGMSPAFISAIV 186 Query: 182 IVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFALMGALAGIAALFQVSR 241 IVI+ LVLT+TVLGR+WIGIGTNEEAVRL+G+NP P K+L FALMG LAG+ ALFQVSR Sbjct: 187 IVIVGHLVLTKTVLGRHWIGIGTNEEAVRLAGINPRPPKVLVFALMGLLAGVGALFQVSR 246 Query: 242 LEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIISVLEAGLAQVGVSEPM 301 LEAADPNGGVGMELQVIAAVVIGGTSLMGGRGS++STFIGVLIISVLEAGLAQVGVSEPM Sbjct: 247 LEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSVISTFIGVLIISVLEAGLAQVGVSEPM 306 Query: 302 KRIITGAVIVVAVILDTYRRRGQR 325 KRIITG VIV AV+LDTYRRRG+R Sbjct: 307 KRIITGLVIVAAVVLDTYRRRGER 330 Lambda K H 0.325 0.137 0.392 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: 412 Number of extensions: 13 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: 328 Length of database: 333 Length adjustment: 28 Effective length of query: 300 Effective length of database: 305 Effective search space: 91500 Effective search space used: 91500 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: 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