GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02713 H281DRAFT_02713 monosaccharide ABC transporter substrate-binding protein, CUT2 family

Query= TCDB::G4FGN5
         (343 letters)



>FitnessBrowser__Burk376:H281DRAFT_02713
          Length = 313

 Score =  138 bits (347), Expect = 2e-37
 Identities = 103/325 (31%), Positives = 154/325 (47%), Gaps = 53/325 (16%)

Query: 20  SEDMTILLAPKSLNNPYWFAVENGMKDAAEKLGIKAIFDAPVEADAAKQAEKILSYIVKG 79
           ++D+++ + PK +  P++     G K AA K G+K  +  P     + Q + I   I + 
Sbjct: 28  AKDISVAVIPK-VAVPFFDDCNKGAKTAAGKAGVKYQWVVPQNTQGSTQVQIIEDLISRH 86

Query: 80  VDGIGISPNDPEGIKVVVKRALDKGIPVIMFDSDSPDSGRYAYIGTNNYNAGYEAGKLMA 139
           VDGI IS N+P+ ++ V+KRA   GI V+ +DSDSP SGR  YIGTNN  AG    + M 
Sbjct: 87  VDGIAISVNEPKSVESVMKRAEQSGIKVLTYDSDSPRSGRSMYIGTNNEQAGATMAETMG 146

Query: 140 QLIEKYKAEKKTIRLAILTGGLAALNLNERIRGFKDALEDYSKRSGKEIVYVADPFPCDD 199
                 KA      +AI+TG L A+NLNERI G K  L  Y        + + +    DD
Sbjct: 147 ------KALNGQGEVAIITGQLGAVNLNERIAGIKKGLAKYPG------IKIVETQGTDD 194

Query: 200 DSAKAIQIIRDVTRKYTDLDGWFMSGGWPLFAPKETVISALGGPERMK------------ 247
           D A+ + ++    R +  L G F              +S +GGP   K            
Sbjct: 195 DLARGVSVVETTLRAHPQLKGIF-------------GVSQVGGPAVAKVLNTKEFGTMKG 241

Query: 248 DLLVVGFDTLLPELELVKAGAVKGLVGQRPYDMGYLSVLVLYNMAKIGVENTLKMLPKVV 307
            L V+ FD L   L+ +K G ++G++ QRP  MG L+V               + L   +
Sbjct: 242 KLEVLAFDDLPDTLKGLKEGYIQGIMVQRPVTMGSLAV---------------EHLVAQI 286

Query: 308 KEDGTVDYIIDTGVDIVTEENVDQF 332
           +        IDTGV +VT++N+  +
Sbjct: 287 QGQEAQPKDIDTGVTVVTKDNMTSY 311


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: 251
Number of extensions: 15
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: 343
Length of database: 313
Length adjustment: 28
Effective length of query: 315
Effective length of database: 285
Effective search space:    89775
Effective search space used:    89775
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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