GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Rhizobium freirei PRF 81

Align Putative beta-xyloside ABC transporter, permease component, 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_004129723.1 RHSP_RS32355 hypothetical protein

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_000359745.1:WP_004129723.1
          Length = 324

 Score =  249 bits (637), Expect = 5e-71
 Identities = 140/303 (46%), Positives = 192/303 (63%), Gaps = 2/303 (0%)

Query: 11  AGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDLSVGSI 70
           AG++L  + ++V LG     F T  N+  V+     IA+++FG T VI   GIDLSVGS 
Sbjct: 22  AGVYLAFVVLLVALGFAAPRFFTFGNLTDVLRQAVPIAVIAFGTTFVIGMRGIDLSVGST 81

Query: 71  LGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGMLSVGR 130
           L  + +V   L+   G    L+   G+AVG   GL NG+LITK  +  FI+T+ ++ + R
Sbjct: 82  LALSGLVTANLI-VLGYPVPLACAGGIAVGAVIGLVNGILITKVGITDFIATMAIMVISR 140

Query: 131 GLAYVMSGGWPISPFPE-SFTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTVTGRRIYA 189
           G+  V + G PI    + +F + GQ   G VPVPVI  A++  IA   L YT  GR + +
Sbjct: 141 GIVMVYTQGIPIVGASDPAFRMIGQSYAGGVPVPVILTAIVFAIAFYLLYYTRFGRFVLS 200

Query: 190 IGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYELDVIAAT 249
           IG N +A++LVGI TD++ I VY + G L+AFAG LLT+ L  A P AGQGYELDVIAA 
Sbjct: 201 IGSNPDAARLVGIPTDKVKIAVYVLVGVLSAFAGVLLTSRLEAAMPEAGQGYELDVIAAV 260

Query: 250 VIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAIAIDQIRR 309
           VIGGT LSGG  T+ G  +GAV+M V+RN + LL V++FW QVVIG +I+IA+A D+  R
Sbjct: 261 VIGGTGLSGGRATLFGTAVGAVLMAVVRNALNLLNVNTFWHQVVIGTIILIAVAADRFSR 320

Query: 310 AKE 312
            ++
Sbjct: 321 RQK 323


Lambda     K      H
   0.328    0.145    0.421 

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: 329
Number of extensions: 15
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: 313
Length of database: 324
Length adjustment: 27
Effective length of query: 286
Effective length of database: 297
Effective search space:    84942
Effective search space used:    84942
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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.

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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