Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_4386 Inositol transport system sugar-binding protein
Query= TCDB::P0AEE5 (332 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386 Length = 308 Score = 120 bits (302), Expect = 3e-32 Identities = 93/312 (29%), Positives = 145/312 (46%), Gaps = 29/312 (9%) Query: 23 AADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKG 82 AA RIGV+I + DDNFM+ VR +E DA +VQ+ D+Q D +Q +Q+ L + Sbjct: 20 AASYRIGVSIARVDDNFMTYVRSGLE-DAARKENVQIQFEDAQGDVVRQLNQVQGFLGQK 78 Query: 83 VKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQ 142 V A+ + VD AA + A +P+V+ N+ P + L V ++ E+G +Q Sbjct: 79 VDAVIVLPVDTAATANMTRAAVEAKIPLVYVNRHPDERVLPK--GVVTVASNDVEAGQLQ 136 Query: 143 GDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELND-KGIKTEQLQL 201 +A+ A G+ ++KG+ + RT V + L D GIK + Q Sbjct: 137 MRYLAEKMA----------GKGNIAIIKGDLAQNSTQDRTEGVNQVLKDYPGIKIVEQQ- 185 Query: 202 DTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKS--SIPVFGVD 259 +A W + D WL + ++ANND MA+GA AL+ K+ I + G+D Sbjct: 186 -SAEWQRNKGMDLTSNWLLA--GADFDAIVANNDEMAIGAAMALQQAGKAKGEIAIVGID 242 Query: 260 ALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYV 319 LP+ LA +K G L +V D QA + A + G+ V VP+ Sbjct: 243 GLPDGLAAIKRGMLVASVFQDPKAQATSALQAAIKMIKGEPVETD---------VWVPFQ 293 Query: 320 GVDKDNLAEFSK 331 + D +A F + Sbjct: 294 LITPDQVAVFEQ 305 Lambda K H 0.313 0.129 0.363 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: 245 Number of extensions: 12 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: 332 Length of database: 308 Length adjustment: 28 Effective length of query: 304 Effective length of database: 280 Effective search space: 85120 Effective search space used: 85120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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