Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_049992209.1 LT39_RS19805 sugar ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >NCBI__GCF_000784335.1:WP_049992209.1 Length = 317 Score = 116 bits (291), Expect = 7e-31 Identities = 72/234 (30%), Positives = 124/234 (52%), Gaps = 12/234 (5%) Query: 94 LDNYAQMASEPKFWEAMRNNMFWLIVVPALSTAFGLLAAQLTDR-IKWGNVAKSIIFMPM 152 L+ Y + + F EA NN LI +S A GL A L D I++ + ++I +PM Sbjct: 78 LEMYREALASEAFREAAFNNFVLLIAFTTISLALGLFLAILLDHGIRYKDKIQTIYLLPM 137 Query: 153 AISFVGASVIWKLVYDGRPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWV 212 A+SFV + +W +++ + G+L I+ LG +P+ +L P ++ LVW Sbjct: 138 ALSFVVTAQLWLWMFN------PESGVLTVIVTTLGFEPIDWLGNPRLALPAVIFALVWQ 191 Query: 213 QTGFAMVILSAALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLK 272 +G+AMV+ A L+ IP + EAA +DGAS ++ + +I VPQ+ + V + + LK Sbjct: 192 FSGYAMVVYLAGLQSIPADQFEAANVDGASTIRTYLRIIVPQLKESSVSAAVVLMVFALK 251 Query: 273 VFDIVFAMTNGQWE----TQVLANYMFDKLFRANDWGVGSASAMVIMLLVTPIL 322 F ++++ GQ+ T +LA M + F+ W G+A A +++LL ++ Sbjct: 252 AFTFLYSLV-GQYRPPNGTDILATLMVRQAFKFGKWAYGAAIATMLLLLALSVI 304 Lambda K H 0.329 0.143 0.455 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: 241 Number of extensions: 14 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: 334 Length of database: 317 Length adjustment: 28 Effective length of query: 306 Effective length of database: 289 Effective search space: 88434 Effective search space used: 88434 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: 48 (23.1 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