Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_012385744.1 BIND_RS14240 rhizopine-binding protein
Query= TCDB::P0AEE5 (332 letters) >NCBI__GCF_000019845.1:WP_012385744.1 Length = 281 Score = 144 bits (362), Expect = 3e-39 Identities = 99/298 (33%), Positives = 154/298 (51%), Gaps = 27/298 (9%) Query: 35 YDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPA 94 +DDN+++V+R+A+E AK DV + D+Q D ++Q QID +A GV A+ + LVD Sbjct: 4 FDDNYLTVLRQAMENYAKTKGDVTVRSEDAQGDIARQQSQIDNFIASGVNAIIVMLVDAD 63 Query: 95 AAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQ 154 ++ + +A VP+VF N+ P D K +VG+D +G +QG + K Sbjct: 64 SSAAISSQAEAAGVPLVFVNQAPVN---DLPTKQAFVGSDEVLAGNMQGQEVCK------ 114 Query: 155 GWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQL-QLDTAMWDTAQAKD 213 +L G++ V+L+G+ G RT V + L+ K ++ TA W A D Sbjct: 115 --ELKGTGKV--VILEGQLGTTGQRGRTEGVHQALSAPACKNIKIVDEKTANWMRTPAMD 170 Query: 214 KMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNK--SSIPVFGVDALPEALALVKSG 271 + W+S V+ANND MA+GAV+ALKA + +S+ + G DA +ALA +K+G Sbjct: 171 LVTNWISA--GLDFNAVLANNDEMALGAVQALKASGRPMNSVVIAGSDATKDALAAMKAG 228 Query: 272 ALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329 L TV +A Q K D A LA G+ + T +P+ V KDN+ ++ Sbjct: 229 DLGVTVFQNATGQGKGAIDAALKLAKGEAVPNKT---------YIPFELVTKDNMDKY 277 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: 233 Number of extensions: 16 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: 332 Length of database: 281 Length adjustment: 27 Effective length of query: 305 Effective length of database: 254 Effective search space: 77470 Effective search space used: 77470 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 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