GapMind for catabolism of small carbon sources

 

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

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_085635685.1 MGEO_RS05330 ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_002115805.1:WP_085635685.1
          Length = 358

 Score =  142 bits (357), Expect = 2e-38
 Identities = 100/326 (30%), Positives = 166/326 (50%), Gaps = 41/326 (12%)

Query: 21  VLLVLLAIIIFQ---DPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77
           +++++ AIIIF       F S   L+ IL Q  +  ++A   + +I+T G DLS    VG
Sbjct: 48  LIVLVAAIIIFGIALGSKFFSPFALTLILQQVQIVGVLAAAQSLIILTAGIDLS----VG 103

Query: 78  LAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFIT 137
             AV+++ ++         F     +P  + +    AIG  IG +NG +++ + + PFI 
Sbjct: 104 AMAVISSVIMGQ-------FTFRYGLPAPMAVAAGLAIGTAIGALNGWLVSRVKLPPFIV 156

Query: 138 TLGTMIIVYGINSLYY--DFVGASPISG-----------FDSGFSTFAQGFVALGSFRLS 184
           TLG   IV   N L+   + + A  I             F  G +TF  G + +      
Sbjct: 157 TLGMWQIVLAANYLFSRNETIRAQDIEANAPFLHFMGYKFQIGGATFTLGVLVM------ 210

Query: 185 YITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAF 244
                 L+ +   +VL N T +G++++A+G +PEAA+++GV+V   L+ +Y L G   A 
Sbjct: 211 -----ILLVLLLAYVLRN-TAWGRHVYAVGDDPEAAQLAGVDVHKTLMSVYMLVGFICAL 264

Query: 245 GGMLEAGRIGSATNNL--GFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYG 302
            G +  GR GS + +   G M  + +I A V+GG+S  GG G+++G   G +I  V   G
Sbjct: 265 AGWVMIGRFGSVSPSASTGMMGNIQSITAVVIGGISLFGGRGSILGAFFGALIVGVFELG 324

Query: 303 LTYIGVNPYWQYIIKGAIIIFAVALD 328
           L   G +P W +++ GA+II AV++D
Sbjct: 325 LRMAGADPQWTFLLIGALIIAAVSVD 350


Lambda     K      H
   0.327    0.143    0.415 

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: 303
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: 336
Length of database: 358
Length adjustment: 29
Effective length of query: 307
Effective length of database: 329
Effective search space:   101003
Effective search space used:   101003
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: 49 (23.5 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