Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS23385 BWI76_RS23385 sugar ABC transporter permease
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__Koxy:BWI76_RS23385 Length = 300 Score = 125 bits (313), Expect = 2e-33 Identities = 88/305 (28%), Positives = 160/305 (52%), Gaps = 30/305 (9%) Query: 7 ELARKIKLRKRIYKLKRFGVYVILIVITVVLLFPILFTIANSFMSDKEVLDTYQKKIEEV 66 E+AR ++ K ++ YVIL+ + +++L+P+++ + SF + E+ T + Sbjct: 17 EVARTLRREKINASIR----YVILLFVGLLMLYPLVWMFSASFKPNHEIFTTLS-----L 67 Query: 67 EEGESTEFLGFKLIPDMVSMKQYYTVLFRKPTFLLMFLNSAIMTIPIVIIQVIVGVFAAY 126 +T + GF I + +Y F LN+ IP V++ +I AY Sbjct: 68 WPAHAT-WDGF--INGWKTGTEY--------NFGHYMLNTFKYVIPKVLLTIISSTIVAY 116 Query: 127 AFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPNYILLRKLDMIGSFLSVILPGGFS--AFG 184 FA+ P + F I ML+P V L+P Y++ R++ M+ S+L + LP F+ F Sbjct: 117 GFARFEIPWKKFWFATLITTMLLPSTVLLIPQYLMFREMGMLNSYLPLYLPLAFATQGFF 176 Query: 185 VVLLRQYMRGIPDECCEAAMIDGAGYLKTFTKIILPQCKSIIASLAILAFIDNWNMVEQP 244 V +L Q++RG+P + EAA IDG ++ +++P K I S+A+ F+ + N P Sbjct: 177 VFMLIQFLRGVPRDMEEAAQIDGCNSIQVLWYVVVPILKPAIISVALFQFMWSMNDFIGP 236 Query: 245 LIFLSDSAKYPLSVYLAY---INEG---DLGLAFASGVLYMIPTVLIYLYGEKYFVEGIQ 298 LI++ KYP+++ L + EG + LA AS + ++P+++++ ++YFV+G+ Sbjct: 237 LIYVYSVDKYPIALALKMSIDVTEGAPWNEILAMAS--ISILPSIIVFFLAQRYFVQGVT 294 Query: 299 LTGIK 303 +GIK Sbjct: 295 SSGIK 299 Lambda K H 0.331 0.147 0.425 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: 216 Number of extensions: 13 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: 303 Length of database: 300 Length adjustment: 27 Effective length of query: 276 Effective length of database: 273 Effective search space: 75348 Effective search space used: 75348 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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