Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate WP_110804792.1 C8J30_RS05885 amino acid ABC transporter substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >NCBI__GCF_003217355.1:WP_110804792.1 Length = 338 Score = 309 bits (791), Expect = 8e-89 Identities = 151/320 (47%), Positives = 213/320 (66%), Gaps = 3/320 (0%) Query: 41 SNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYRS 100 S S L+ V+ARG+L+CGV L GF D+ GNY G DV CKA+AAA+ DP ++Y++ Sbjct: 21 SASTLDDVKARGQLICGVNPGLTGFGAPDANGNYQGFDVAACKAVAAAVLGDPMKVQYKA 80 Query: 101 LDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQSL 160 L RF ALASGEVD+L+RN+TWT RD + L+F +YDGQG MV ++ G+ S Sbjct: 81 LTGETRFTALASGEVDMLARNSTWTFGRDTELA--LDFVAVNYYDGQGFMVNKSLGVSSA 138 Query: 161 QDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRSQ 220 ++ G ++CV+TGTT+E+NLAD + + Y + + + G C+ T+D S Sbjct: 139 KELDGATVCVQTGTTTEMNLADYFKSNNMTYTPVNIADDAEGQQKFLAGACDSYTTDASG 198 Query: 221 LAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQAN 280 LAA R T+ +A +L +ISKEPL+ A + D+ W D+V+W A + AEE+GIT+AN Sbjct: 199 LAASRATMPNAADIVILPEIISKEPLALAVRHGDNNWGDIVRWSFYALVAAEEYGITKAN 258 Query: 281 IDQFKTS-KNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLKL 339 +++ S +NPEIRR LGLEG++G+++GL NDFA RAI A GNYGEI+E N+G + + L Sbjct: 259 LEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIMASGNYGEIFEANIGASTSIGL 318 Query: 340 NRGLNQLYKNGGLLYSPPFR 359 RGLN + GGL+Y+PPFR Sbjct: 319 ARGLNAQWTQGGLMYAPPFR 338 Lambda K H 0.317 0.134 0.391 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: 318 Number of extensions: 10 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: 359 Length of database: 338 Length adjustment: 29 Effective length of query: 330 Effective length of database: 309 Effective search space: 101970 Effective search space used: 101970 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: 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