GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sulfurimonas denitrificans DSM 1251

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  229 bits (584), Expect = 2e-64
 Identities = 153/459 (33%), Positives = 239/459 (52%), Gaps = 17/459 (3%)

Query: 27  VNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEI 86
           VNP    V S      A+DA+KA++ A  A  E       +R SWL  +++ + +   +I
Sbjct: 21  VNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDI 80

Query: 87  SALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPG---ENILLFKRA- 142
           +  I +E GK    + +EV    + +   AE  R   GE + +D      + I  F R  
Sbjct: 81  AKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140

Query: 143 LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLP-RGV 201
            GV   I P+NFP  LIA K+APAL+ GN +++KP+   P  A  FAK+  E     +  
Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200

Query: 202 FNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVM 261
            ++V G  + VG  L  +    ++S TGSV  GE I  T +  I KV LELGG A   + 
Sbjct: 201 LSVVYGDAD-VGGTLVTSEIPRVISFTGSVGVGEII--TKSAGIKKVSLELGGNAATFID 257

Query: 262 DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERN 321
             A+L+LA +       +NSGQVC   +R+YV K IY +F  ++ EA + +  G+P E  
Sbjct: 258 KSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE-E 316

Query: 322 DIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMH 381
           D  MGPL+N  A +R  + V  A++EGA      + VEG+ +Y  P ++ DV+++M+I+ 
Sbjct: 317 DTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPR-VEGRVFY--PCVMADVKEDMAIVC 373

Query: 382 EETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYIN--- 438
           +E F P++ ++     ++A+ M N+S YGL  SI+T +LN+  +AI  L  G   IN   
Sbjct: 374 QEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMP 433

Query: 439 RENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
              F+     + G + SG+G    +  + E  + + V +
Sbjct: 434 TLRFDIQP--YGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.318    0.135    0.392 

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: 468
Number of extensions: 22
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: 479
Length of database: 471
Length adjustment: 33
Effective length of query: 446
Effective length of database: 438
Effective search space:   195348
Effective search space used:   195348
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