Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_011610610.1 TERY_RS03790 galactose/glucose ABC transporter substrate-binding protein MglB
Query= TCDB::P0AEE5 (332 letters) >NCBI__GCF_000014265.1:WP_011610610.1 Length = 342 Score = 365 bits (936), Expect = e-105 Identities = 193/336 (57%), Positives = 248/336 (73%), Gaps = 15/336 (4%) Query: 3 KKVLTLSAVMASMLF-GAAAHAADTR-----IGVTIYKYDDNFMSVVRKAIEQDAKAAPD 56 KK L +++++AS+LF G A+ ++ + IGVTIYKYDDNFMS VR+ IE A A Sbjct: 2 KKSLFIASILASLLFIGCTANTSNNKENLIKIGVTIYKYDDNFMSYVRRYIESSANAK-- 59 Query: 57 VQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKE 116 +L +NDSQN+Q+KQ +QID ++AKGVKALAINLVDP +A TVI KA+ N+PV+FFNKE Sbjct: 60 ARLFINDSQNNQAKQLEQIDTMIAKGVKALAINLVDPKSAITVIAKAKKANLPVIFFNKE 119 Query: 117 PSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAAN-QGWDLNKDGQIQFVLLKGEPGH 175 P + L+SY+K++YVGT+S+ESGIIQG +I W N + WDLN+DG+IQ+VLLKGEPGH Sbjct: 120 PELELLNSYEKSWYVGTNSQESGIIQGTIITNLWNKNKEQWDLNQDGKIQYVLLKGEPGH 179 Query: 176 PDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANND 235 PDAEART YVI E+ GI+ E+L +DTAMWD +A +KMD W+S NKIE+VIANND Sbjct: 180 PDAEARTKYVIDEVKKAGIEVEKLAIDTAMWDATKAANKMDVWIS-KYGNKIELVIANND 238 Query: 236 AMAMGAVEALKA----HNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDL 291 AMA+GA+ +L+ + +P+ GVDA+PE L ++ G + GTVLNDA NQ KATFDL Sbjct: 239 AMALGALSSLEKAGYFKDNKLVPIVGVDAIPEVLIKIREGKIVGTVLNDAKNQGKATFDL 298 Query: 292 AKNLADGKGAADGTNWKID-NKVVRVPYVGVDKDNL 326 A N A GK T WK+D NK V VPYV + KDNL Sbjct: 299 AFNAALGKDILADTQWKLDVNKAVLVPYVSITKDNL 334 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: 412 Number of extensions: 15 Number of successful extensions: 7 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: 342 Length adjustment: 28 Effective length of query: 304 Effective length of database: 314 Effective search space: 95456 Effective search space used: 95456 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: 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