GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Stenotrophomonas chelatiphaga DSM 21508

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_057508189.1 ABB28_RS08325 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= BRENDA::G5CZI2
         (498 letters)



>NCBI__GCF_001431535.1:WP_057508189.1
          Length = 892

 Score =  118 bits (295), Expect = 1e-30
 Identities = 93/297 (31%), Positives = 134/297 (45%), Gaps = 8/297 (2%)

Query: 3   TIGHLINGQLVTENTRSQNVFNPA-TGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTPP 61
           T   L+ G  VT    S  V NPA T ++      A   TV++A++ A  A P W  TP 
Sbjct: 586 TAAPLVPGATVTG--ASLPVTNPADTRQVVGHWQAADAATVQKALANAVAAQPAWNRTPA 643

Query: 62  LKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEY-ACGAPELLKG 120
             RA ++    + LE    E   L  +E GK   D + E++  ++ + Y A  A E    
Sbjct: 644 TSRAAILEHAADQLEARIAEFMALCVKEAGKSLPDGVAEVREAVDFLRYYAKQAREQFAH 703

Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180
                   G  +  +    GV   I+P+NFP+ + L     A+  GN  + KP+E+    
Sbjct: 704 AEKLPSPTGESNELQLHGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTNLI 763

Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVD-ALLHDDRVKAVSFVGSTPIAEYIYRTASAN 239
             Y  +LL +AG+P+GV+  + GD   V  AL  D RV  V+F GST  A  I R  +A 
Sbjct: 764 GYYAVKLLLDAGVPEGVLQFLPGDGATVGAALTADPRVAGVAFTGSTDTARAINRAMAAR 823

Query: 240 GKRCQAL---GGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAA 293
                 L    G +N  I    A  +  V   +G+AF S+G+RC A  V     D A
Sbjct: 824 DAAIGVLIAETGGQNAFIADSSALPEQLVKDAIGSAFTSAGQRCSAARVLFVQDDIA 880


Lambda     K      H
   0.319    0.135    0.405 

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: 891
Number of extensions: 52
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: 498
Length of database: 892
Length adjustment: 38
Effective length of query: 460
Effective length of database: 854
Effective search space:   392840
Effective search space used:   392840
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 (21.7 bits)
S2: 54 (25.4 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