GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Sulfurimonas denitrificans DSM 1251

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-13361
         (500 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  221 bits (562), Expect = 6e-62
 Identities = 140/469 (29%), Positives = 244/469 (52%), Gaps = 27/469 (5%)

Query: 38  INPVNGKLISDVFEADA----KQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQA 93
           +NP NG++ S+    +A    K +N A++A++ A      K ++  R + +  +A  +  
Sbjct: 21  VNPYNGEVASEFVTCNADDAKKALNIALLASKEA-----SKTTIAQRCSWLLDVASKLAQ 75

Query: 94  RFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMST-SDGSGALN 152
             E+       + G+P+  +R +++ R I      A+  +T H +       + G   ++
Sbjct: 76  NKEDIAKTITDEVGKPITYSR-IEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTIS 134

Query: 153 YTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAG 212
           +  R P GV+  I+P+N PL L   K+APAL  GN V+ KP+ E+P +A   A++  ++ 
Sbjct: 135 FFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESE 194

Query: 213 VP-PGVFNLIHGFGKDSAGEFLTQH-PGISALTFTGESKTGSTIMKAVADGVKEVSFELG 270
                  ++++G   D  G  +T   P +  ++FTG    G  I K+   G+K+VS ELG
Sbjct: 195 FAIKDALSVVYG-DADVGGTLVTSEIPRV--ISFTGSVGVGEIITKSA--GIKKVSLELG 249

Query: 271 GKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLV 330
           G  A  +   A+LD A +     +F NSGQVC+  +R+YVH+ I+ EF   +    ++LV
Sbjct: 250 GNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLV 309

Query: 331 VGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTI 390
           VG P ++   MGPL++     + + + + A+ EGAT +         + R +G    P +
Sbjct: 310 VGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL--------EPRVEGRVFYPCV 361

Query: 391 WTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQ 450
              + +    V +E+F P+  +    D DE +  +N+S YGL  +I+T +L+   R   +
Sbjct: 362 MADVKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINE 421

Query: 451 IHVGLVWVNTW-YLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498
           +  G + +N    LR    P+GGVKLSG+GREG RF+++  S+I ++ I
Sbjct: 422 LDAGGIVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.318    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: 483
Number of extensions: 17
Number of successful extensions: 5
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: 500
Length of database: 471
Length adjustment: 34
Effective length of query: 466
Effective length of database: 437
Effective search space:   203642
Effective search space used:   203642
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: 52 (24.6 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