GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Corynebacterium deserti GIMN1.010

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_082353398.1 CDES_RS06155 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_001277995.1:WP_082353398.1
          Length = 513

 Score =  263 bits (671), Expect = 1e-74
 Identities = 156/459 (33%), Positives = 236/459 (51%), Gaps = 7/459 (1%)

Query: 23  NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82
           NPA    V A +   T   V  A++ A A    W  T   +R +++ K  E++     E 
Sbjct: 44  NPAT-GAVTASLPFATTATVNAAVSAAQAVAPAWRATGLARRAAVMFKLHEIITSRKDEL 102

Query: 83  ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142
           A L+T E+GK L D+  E+ R    ++F   L   + G+ L  A     +  V++PLGVV
Sbjct: 103 AALITEEQGKVLSDAAGEIARGLENVEFCAGLVHHMKGEFLEQAAAGLDVHQVRQPLGVV 162

Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202
           A ITP+NFP  +P+W +  A+AAGNT V+KP+ K P  V  +VE   +AGLPEGV+NL+ 
Sbjct: 163 ACITPFNFPAMVPLWMITTAIAAGNTVVLKPSEKDPSAVNWIVEAFHEAGLPEGVLNLIH 222

Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262
           G   E  + ++ D  + AVSF GST + + IY       +  R+Q   G KN + V   A
Sbjct: 223 G-DREAVEALIDDPRVQAVSFVGSTPIAQSIYTRATALGK--RVQALGGAKNHMVVMPDA 279

Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPGTE-DVDM 321
           DL  AA+ AV  G+G  G+ C A S ++   D+      ++  R+    +G GT+ D +M
Sbjct: 280 DLDAAADAAVSAGYGAAGERCMAISVVVPVGDIADDLIAKISSRITDLTIGEGTDPDSEM 339

Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEPTIFEGVTSDMRLFKEE 379
           GPV+     ++    I    + GA+++  G  +  P +G+F+ PT+ + V   M ++ EE
Sbjct: 340 GPVITSAAKERIEGLIAGSSDSGAEVVVDGRSVDLPDEGFFIGPTLIDHVKPGMPVYDEE 399

Query: 380 IFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVG 439
           IFGPVLSV      DEA+ L+N+  Y +   I   D +   EF   +E G++ +N P   
Sbjct: 400 IFGPVLSVARVGHFDEAVELINSCQYANGTAIFTRDGRTAREFEFAIEVGMVGINVPIPV 459

Query: 440 LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478
                 FGG+K S        G ++  FY + K V   W
Sbjct: 460 PIGAFSFGGWKKSLFGDTHMYGPESFNFYTRRKVVTSRW 498


Lambda     K      H
   0.316    0.135    0.389 

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: 600
Number of extensions: 31
Number of successful extensions: 6
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: 478
Length of database: 513
Length adjustment: 34
Effective length of query: 444
Effective length of database: 479
Effective search space:   212676
Effective search space used:   212676
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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