GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Rhizorhabdus wittichii RW1

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= TCDB::Q8YPM8
         (308 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score =  148 bits (373), Expect = 2e-40
 Identities = 70/133 (52%), Positives = 96/133 (72%)

Query: 172 TFSPEFSALLLGLIFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQAL 231
           T +PEF A+L G + Y  AF AEIVRGG+  V +GQWEA R+LGL+    +RLVI PQAL
Sbjct: 238 TLTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQAL 297

Query: 232 RVIIPPLTSQYLNLTKNSSLAIAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLT 291
           R+I+PP+ SQ++ + KNS+LA+ +GYPD+ FVA+T  N TG+ +E + +LML + +L+  
Sbjct: 298 RMIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASA 357

Query: 292 ISLIMNAFNRTVQ 304
           ISL MN  N  VQ
Sbjct: 358 ISLAMNRLNARVQ 370



 Score = 90.1 bits (222), Expect = 7e-23
 Identities = 46/135 (34%), Positives = 79/135 (58%), Gaps = 1/135 (0%)

Query: 15  WYIAGQLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDT 74
           W++    + L LA  V+ ++   ++ N++R  +     FL+  A F I E+ +AY P DT
Sbjct: 12  WWLPQVALLLALAGLVL-VVARTVSDNMERQDMVLSLGFLRSTAEFPIAESFLAYAPGDT 70

Query: 75  YSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQ 134
            + A  VGL NS+ +  + I+L+T+ G+   +AR S + L R ++  +V++ RN PL++Q
Sbjct: 71  IAWAFVVGLGNSIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQ 130

Query: 135 LLFWYFAVFLGLPRA 149
           LLFWY  + +  P A
Sbjct: 131 LLFWYGVILMAFPPA 145


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: 291
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 308
Length of database: 374
Length adjustment: 28
Effective length of query: 280
Effective length of database: 346
Effective search space:    96880
Effective search space used:    96880
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 Apr 09 2024. 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