GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Sulfurimonas denitrificans DSM 1251

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  187 bits (475), Expect = 7e-52
 Identities = 133/437 (30%), Positives = 210/437 (48%), Gaps = 11/437 (2%)

Query: 27  VNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRARILFNFQQLLSQHKEEL 86
           VNP   EV  +      +D   A   A  A K  SK  + +R   L +    L+Q+KE++
Sbjct: 21  VNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDI 80

Query: 87  AHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS--IATDVEAANY--RYP 142
           A  IT E GK    +  EV R IE V  AA     M G+++ +   A+  +  ++  R P
Sbjct: 81  AKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140

Query: 143 IGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVELF-EKAGLPKGV 201
            GVV  I PFNFP+ +       A+  GN  ILKP+   PL   K  +LF E     K  
Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200

Query: 202 FNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQSLTGAKNHTIVLN 261
            +VVYG  DV   ++     + ISF GS  VGE + K  S  +K+V    G    T +  
Sbjct: 201 LSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITK--SAGIKKVSLELGGNAATFIDK 258

Query: 262 DANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVADIKIGNGLDDGV 321
            ANL+         AF ++G+ C++   + V + I  EF  K+ E    + +G+  ++  
Sbjct: 259 SANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEEDT 318

Query: 322 FLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIFDNVTTEMTIWKD 381
           F+GP++ ++  KR + +++  ++EGA  + + R     +G    P +  +V  +M I   
Sbjct: 319 FMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRV----EGRVFYPCVMADVKEDMAIVCQ 374

Query: 382 EIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENIDAGMLGINLGVP 441
           E+FAP++S+I VK+  EA+ + N S +     +FT++ N  +     +DAG + IN    
Sbjct: 375 EVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMPT 434

Query: 442 APMAFFPFSGWKSSFFG 458
                 P+ G K S  G
Sbjct: 435 LRFDIQPYGGVKLSGVG 451


Lambda     K      H
   0.318    0.136    0.396 

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: 494
Number of extensions: 27
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: 487
Length of database: 471
Length adjustment: 34
Effective length of query: 453
Effective length of database: 437
Effective search space:   197961
Effective search space used:   197961
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 (21.7 bits)
S2: 51 (24.3 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