GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Marivita geojedonensis DPG-138

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_085635593.1 MGEO_RS05025 ABC transporter permease

Query= TCDB::G4FGN4
         (313 letters)



>NCBI__GCF_002115805.1:WP_085635593.1
          Length = 324

 Score =  179 bits (454), Expect = 8e-50
 Identities = 105/303 (34%), Positives = 171/303 (56%), Gaps = 6/303 (1%)

Query: 6   FKAREAGIFLILIAIVVFLGVTTREFLTVENIFTVILNVSFIAIMSFGMTMVIITSGIDL 65
           F AR+ GI +     +V   +  + F+  +NI  VI + + + +M+ G+T V+I+  +DL
Sbjct: 12  FLARQ-GILVAFAVFMVGFTLANQRFVDPDNILGVIRSSAILGVMALGVTFVVISGNLDL 70

Query: 66  SVGSILGAASVVMGLLMDEKGLSPFLSVVIGLAVGVGFGLANGLLITKARLAPFISTLGM 125
           SVGS++  +++V+  L D+ G  P L++    A+ +  G   G L+   +L   I TLGM
Sbjct: 71  SVGSMMSFSTIVVLDLHDKIG--PALAIPAMFAMTLCLGAFIGFLVGYLKLNSLIVTLGM 128

Query: 126 LSVGRGLAYVMSGGWPISPFPES---FTVHGQGMVGPVPVPVIYMAVIGVIAHIFLKYTV 182
           LS   GL    SGG  +    +    F   GQG    +PVP++   ++  +  + L  T 
Sbjct: 129 LSAIHGLTLTYSGGQNMDIADKEGTWFDFFGQGSALGIPVPILIFVLLAAVLGVVLSKTP 188

Query: 183 TGRRIYAIGGNMEASKLVGIKTDRILILVYTINGFLAAFAGFLLTAWLGVAQPNAGQGYE 242
            GR++YA+GGN  A+   GI+  R++   Y I+ F  A AG L  +    +Q   GQG E
Sbjct: 189 FGRKVYAVGGNGTAATFSGIRRARVVFTCYLISAFCVATAGLLQASRSLGSQNTVGQGLE 248

Query: 243 LDVIAATVIGGTSLSGGEGTILGAFLGAVIMGVLRNGMILLGVSSFWQQVVIGIVIIIAI 302
           L+V+AA ++GG SL GG GTI    +G +I+G ++NG++L+G+  + Q VV  I+II+A+
Sbjct: 249 LEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLQFYVQYVVTWIIIILAV 308

Query: 303 AID 305
            +D
Sbjct: 309 WLD 311


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: 337
Number of extensions: 22
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