GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Skermanella stibiiresistens SB22

Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_037452166.1 N825_RS13095 ribose ABC transporter permease

Query= TCDB::P23200
         (336 letters)



>NCBI__GCF_000576635.1:WP_037452166.1
          Length = 338

 Score =  193 bits (490), Expect = 6e-54
 Identities = 116/331 (35%), Positives = 188/331 (56%), Gaps = 27/331 (8%)

Query: 2   SALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAG 61
           +A  K++  T ++  G+  VL+++     F    FL+  N+S ++ Q+S+ I++A G+  
Sbjct: 21  AATRKQNLHTIIQVVGMLPVLILICIGFEFATGKFLTARNISIVMQQASINIVLATGLTF 80

Query: 62  LIVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGL 121
           +I+T G DL+ G  + ++AV A ++  +        P++A +P+AL++      G  +G 
Sbjct: 81  VILTGGIDLAVGAVLAVSAVTAVSMTLTG------MPDLA-IPLALLV------GLALGA 127

Query: 122 INGLIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGS- 180
           +NG +IA+  + PFI TLG M  V G++ L          S  D+     A  F  +G+ 
Sbjct: 128 VNGSLIAFFRLPPFIVTLGAMTAVRGLSRL----------SANDTTVFNAALPFAWIGNS 177

Query: 181 --FRLSYITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALS 238
             F + ++   AL  VA  W +  +T  G  I+ +GGNP+AA++SG+ V   LL +YA+S
Sbjct: 178 QLFGIPWMVIIALAVVAISWFVLRRTVLGVWIYGVGGNPDAARLSGIKVWAVLLFVYAIS 237

Query: 239 GVFYAFGGMLEAGRIGSATN-NLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFT 297
           G+     G++ A R  SA    LG  YELDAIAA ++GG SF GG+G++ G + G +I  
Sbjct: 238 GMLAGLAGVMSAARTLSANGAQLGMGYELDAIAAVILGGTSFVGGIGSIFGTLIGALIIA 297

Query: 298 VINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328
           V++ GL  + V+  WQ IIKG +I+ AVALD
Sbjct: 298 VLSNGLILMNVSEVWQLIIKGLVIVGAVALD 328


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: 287
Number of extensions: 18
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: 336
Length of database: 338
Length adjustment: 28
Effective length of query: 308
Effective length of database: 310
Effective search space:    95480
Effective search space used:    95480
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