GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Sinorhizobium meliloti 1021

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate SMc01030 SMc01030 pyruvate dehydrogenase alpha2 subunit protein

Query= BRENDA::A0A222AKA3
         (368 letters)



>FitnessBrowser__Smeli:SMc01030
          Length = 348

 Score =  129 bits (324), Expect = 1e-34
 Identities = 98/329 (29%), Positives = 157/329 (47%), Gaps = 23/329 (6%)

Query: 11  APAPAGPVTAGPVTAAPAA---AAPAAAGVPPDRQLLMYRAMVVGRAFNRQATAFSRQGR 67
           AP  +  V++    A PA    A    A    +  L  YR M++ R F  +A      G 
Sbjct: 2   APRKSASVSSRKTAAKPAKKDFAGGTIAEFSKEDDLKAYREMLLIRRFEEKAGQLYGMGF 61

Query: 68  LAVYPSSR-GQEACQVGSALAVRPTDWLFPTYRESVALLTRGIDPVQV---LTLFRGDQH 123
           +  +     GQEA  VG  LA++  D +   YR+   +L  G+    V   LT  RG   
Sbjct: 62  IGGFCHLYIGQEAVVVGMQLALKEGDQVITGYRDHGHMLACGMSARGVMAELTGRRGGLS 121

Query: 124 CGYD------PVTEHTAPQCTPLATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDF 177
            G           +H       +  Q     GLA A R  G+  V+LAY GDGA ++G  
Sbjct: 122 KGKGGSMHMFSKEKHFYGGHGIVGAQVSLGTGLAFANRYRGNDNVSLAYFGDGAANQGQV 181

Query: 178 HEALNYAAVRRAPVVFLVQNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQV 237
           +E+ N AA+ + PV+++V+NN+YA+   +++ +A    + + A +G+PG ++DG DV  V
Sbjct: 182 YESFNMAALWKLPVIYIVENNRYAMGTSVSRASAQTDFSQRGASFGIPGYQVDGMDVRAV 241

Query: 238 YRAVHDAAERARAGHGPTLIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQ-DPVDRLER 296
             A  +A E  R+G GP ++E +TYR   H +  D  +YR   E     ++ DP+++++ 
Sbjct: 242 KAAADEAVEHCRSGKGPIILEMLTYRYRGH-SMSDPAKYRSKDEVQKMRSEHDPIEQVKA 300

Query: 297 DLLAAG--------VLDRAAADGIAAAAD 317
            L   G         +D+   D +A +AD
Sbjct: 301 RLTDKGWATEDELKQIDKEVRDIVADSAD 329


Lambda     K      H
   0.319    0.132    0.395 

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: 270
Number of extensions: 7
Number of successful extensions: 2
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: 368
Length of database: 348
Length adjustment: 29
Effective length of query: 339
Effective length of database: 319
Effective search space:   108141
Effective search space used:   108141
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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