Align ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_086510093.1 BZY95_RS11660 ABC transporter substrate-binding protein
Query= uniprot:A0A166QFS3 (424 letters) >NCBI__GCF_002151265.1:WP_086510093.1 Length = 421 Score = 519 bits (1337), Expect = e-152 Identities = 252/410 (61%), Positives = 317/410 (77%), Gaps = 3/410 (0%) Query: 17 AGLPSLS--SAADLTISCGAVGAELQLCKEAVQAWSKQTGNNVEVVSTPNSATERLSFYQ 74 AG S S AADLTISCGAVGAELQLC++ V+AW ++TG +V+VVSTPNS+TERLS YQ Sbjct: 13 AGATSFSHAQAADLTISCGAVGAELQLCQQGVRAWEEKTGYSVDVVSTPNSSTERLSLYQ 72 Query: 75 QILSAQSSDIDIIQIDMVWPGMLAKHLLDLREVLPANATQGYFQAQVDNATVNGRLVTMP 134 QILSA S+DIDI+QID+VWPG+LA HLLDLREVL +A +G+F A V+N T++ RLV MP Sbjct: 73 QILSANSTDIDIMQIDVVWPGLLANHLLDLREVLGDDAGEGHFSAIVENNTIDDRLVAMP 132 Query: 135 WFTDSGLLYYRKDLLEKYNQQVPRTWEEMTATARNIQQAERTAGNPNAWGYIFQGRAYEG 194 WFTD+G+LYYR DLLE+Y + P TWEE+T AR IQ AER AGN G++FQGRAYEG Sbjct: 133 WFTDAGVLYYRADLLEQYGFEPPETWEELTEVAREIQNAEREAGNSRMHGFVFQGRAYEG 192 Query: 195 LTCNALEWISSQPEGGLVNSRGDIVVNSQASRTALTLAKSWVGDISPRGVLNYTEEEGRG 254 LTCNALEW++S G +V+ G+I +N+ + AL LA SW+GDISP GVLNYTEEE RG Sbjct: 193 LTCNALEWVASHGGGTIVDQDGEITINNPQAAAALDLAASWIGDISPNGVLNYTEEEARG 252 Query: 255 VFQSGNALFMRNWPYVWALVQGQDSAVKDKVGVAPLPRGGETGTHASTLGGWGLAVSRYS 314 VFQ GNA+FMRNWPY WAL Q + S V+ KVGV LP G+ G+ A+TLGGW LAVSRYS Sbjct: 253 VFQGGNAVFMRNWPYAWALAQSEGSEVRGKVGVTQLPYSGD-GSTAATLGGWNLAVSRYS 311 Query: 315 AHPKLAAELVSYLTSAQEQKHRALIGAYNPVIESLYQDPELLAAMPYYAQLHSILNDGVM 374 +P+LAA+LV++L +EQK RA+ GAYNP +E+LYQD E+L A+P++ +L+ + V Sbjct: 312 ENPELAADLVAFLAGEEEQKRRAIEGAYNPTLEALYQDDEVLEAVPFFGELYETFVNAVA 371 Query: 375 RPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTRIKRRNW 424 RP++ T D Y RVSNAFF H VL+G +QA+++L+ EL R+KRRNW Sbjct: 372 RPSAPTGDAYGRVSNAFFSATHDVLSGNRSGEQAMSDLDHELARLKRRNW 421 Lambda K H 0.316 0.131 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: 509 Number of extensions: 11 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: 424 Length of database: 421 Length adjustment: 32 Effective length of query: 392 Effective length of database: 389 Effective search space: 152488 Effective search space used: 152488 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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