GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Desulfovibrio vulgaris Hildenborough

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q8YPM8
         (308 letters)



>MicrobesOnline__882:206399
          Length = 337

 Score =  137 bits (344), Expect = 5e-37
 Identities = 83/243 (34%), Positives = 133/243 (54%), Gaps = 20/243 (8%)

Query: 63  GETLIAYKPTDTYSLA----LWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNI 118
           G+ + +  P   Y ++    L  GL  +L ++ + II+  ++G++ G+AR+S N  +R +
Sbjct: 107 GDYIYSGDPVGRYEVSKPGILLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWL 166

Query: 119 SLVYVEIFRNTPLLLQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFS 178
           ++ Y+EI R +PLL+Q+  WYF V   L     K+ L     L        W+       
Sbjct: 167 AITYIEIIRGSPLLVQVFLWYFVVGTLLNALFEKVGLSAIPPL--------WYG------ 212

Query: 179 ALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPL 238
             ++ L  +TGA++AEIVR GIQSV +GQ EA RSLG++ +  MR VI PQA R I+PPL
Sbjct: 213 --VMALAIFTGAYVAEIVRAGIQSVHRGQMEAARSLGMSYAQSMRKVILPQAFRRIMPPL 270

Query: 239 TSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNA 298
             Q+++L K+SSL   I   ++          + +  E+ ++  L YL L+ T+SL +  
Sbjct: 271 AGQFISLVKDSSLLGVIAVRELTKATREVVTTSLQPFELWIVCALLYLVLTFTLSLCVQY 330

Query: 299 FNR 301
             R
Sbjct: 331 LER 333


Lambda     K      H
   0.328    0.143    0.430 

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: 282
Number of extensions: 20
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: 308
Length of database: 337
Length adjustment: 28
Effective length of query: 280
Effective length of database: 309
Effective search space:    86520
Effective search space used:    86520
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 17 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