Align LacI family transcriptional regulator, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_040639047.1 MICLODRAFT_RS20115 sugar ABC transporter substrate-binding protein
Query= TCDB::G4FGN5 (343 letters) >NCBI__GCF_000262405.1:WP_040639047.1 Length = 311 Score = 163 bits (412), Expect = 6e-45 Identities = 111/307 (36%), Positives = 162/307 (52%), Gaps = 32/307 (10%) Query: 27 LAPKSLNNPYWFAVENGMKDAAEKLG-IKAIFDAPVEADAAKQAEKILSYIVKGVDGIGI 85 + PK++NNPY+ +G A++LG ++ I+ PVE + A QA+ I I + VDGI I Sbjct: 28 IVPKAMNNPYFDLSRDGCMKRAKELGNVECIYKGPVEHEPASQAQIIQDLISQKVDGIAI 87 Query: 86 SPNDPEGIKVVVKRALDKGIPVIMFDSDSPDSGRYAYIGTNNYNAGYEAGKLMAQLIEKY 145 S +D V+K A D GIPVI FD+D+P+S R A++GT+N G G+ E Sbjct: 88 SVSDAAAAVRVIKSARDAGIPVITFDADAPNSARQAHVGTDNRAMGRALGE------ELL 141 Query: 146 KAEKKTIRLAILTGGLAALNLNERIRGFKDALEDYSKRSGKEIVYVADPFPCDDDSAKAI 205 K + + A+++GG AA NL ER+ G +DAL + K P C+DD A A+ Sbjct: 142 KLRPEGGKYAMVSGGPAAANLKERVEGVRDAL-----KGSKWTEVSGSPTYCNDDLALAV 196 Query: 206 QIIRDVTRKYTDLDGWFMSGGWPLFAP---KETVISALGGPERMKDLLVVGFDTLLPELE 262 Q ++D+ DL GGWP+F P K V ++ K LVV DTL +LE Sbjct: 197 QQMQDLKTANPDLAAIVPVGGWPMFVPEAYKSFVNKNKEAMDQGKFSLVVA-DTLKVQLE 255 Query: 263 LVKAGAVKGLVGQRPYDMGYLSVLVLYNMAKIGVENTLKMLPKVVKEDGTVDYIIDTGVD 322 L++ G LVGQRPY+MG ++ +L + K+ V I+ G+D Sbjct: 256 LLRDGYANALVGQRPYEMGEKAMDILMQL----------------KKGEKVQDIVYAGID 299 Query: 323 IVTEENV 329 VT++NV Sbjct: 300 RVTKDNV 306 Lambda K H 0.318 0.139 0.398 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: 260 Number of extensions: 15 Number of successful extensions: 6 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: 343 Length of database: 311 Length adjustment: 28 Effective length of query: 315 Effective length of database: 283 Effective search space: 89145 Effective search space used: 89145 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 (21.7 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