Align ABC transporter permease (characterized, see rationale)
to candidate HSERO_RS08915 HSERO_RS08915 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__HerbieS:HSERO_RS08915 Length = 296 Score = 172 bits (437), Expect = 7e-48 Identities = 102/305 (33%), Positives = 175/305 (57%), Gaps = 17/305 (5%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MDILLQ + +G+ LG +YA+IA GY + + +NF GE LM+GAL S +G + G Sbjct: 1 MDILLQLVFSGIALGMIYAVIAFGYQLTFATSGTLNFGQGEALMLGALVGLSVVGNIHGG 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRP-LRSSPRLAPLITAIGMSILLQTLA 119 P W+++ I V A +E + RP ++ +++ I ++I+ + +A Sbjct: 61 -PYLNYWLMIP----IVLVFGALQGMFVEWIGVRPAIKIKSEFGWIMSTIALAIIFKNVA 115 Query: 120 MIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNL-GRAMR 178 IW + P+P+ + +PF+I GA + P Q+L++ V A+ + + V L N ++ G+A+ Sbjct: 116 ENIWGKDDLPFPSPISGAPFQIFGANVQPMQVLVV-VGALLIMAAVELFNRKSIYGKAVV 174 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 AT+ + A LMG+ MVI+ ++ + + AA AG++ A T TMG GLKAF Sbjct: 175 ATSNDRDAAGLMGINTSMVITFSYALSSATAAFAGVLVAPLTLTGA-TMGAALGLKAFAV 233 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 A+ GG+ + GA+VGG++LG+ E TLTG + + Y ++ ++L+++L ++P+ Sbjct: 234 AIIGGLTSGMGAIVGGLILGVAE--------TLTGFYISTGYKEVPGLVLLLLVLAVKPA 285 Query: 299 GLLGE 303 GL G+ Sbjct: 286 GLFGK 290 Lambda K H 0.327 0.142 0.419 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: 209 Number of extensions: 15 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: 309 Length of database: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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 (21.7 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