GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Sulfurimonas denitrificans DSM 1251

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= uniprot:Q92L07
         (510 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  159 bits (401), Expect = 3e-43
 Identities = 132/446 (29%), Positives = 214/446 (47%), Gaps = 20/446 (4%)

Query: 37  SPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLG 96
           +P  GE  +   T +A +A   +  A  A +        +R   +  +  +L   K D+ 
Sbjct: 22  NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81

Query: 97  RLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATER--PGHRMMETWH--PL 152
           + ++ E GK  +    EV+  I+    A    R ++G T+ T+    G + +  +   P 
Sbjct: 82  KTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVPC 141

Query: 153 GVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAP 212
           GVV  I+ FNFP+ + +   A ALV G+AV+ KP+ + PLTA     +   +     DA 
Sbjct: 142 GVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA- 200

Query: 213 EGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGI 272
                V+ GD  +G  LV      ++S TGS  +G  +      +  +  LELGGN A  
Sbjct: 201 ---LSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITKSAGIK--KVSLELGGNAATF 255

Query: 273 VCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLE 332
           +  SA+LD+A +  A GA   +GQ C +L+R++VH+ +Y +   ++ +A + + VG+P E
Sbjct: 256 IDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE 315

Query: 333 SAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGHENGYYVKPALVEMPKQE-G 391
               +GPLV+  A     + +  A   G       RVE     G    P ++   K++  
Sbjct: 316 EDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRVE-----GRVFYPCVMADVKEDMA 370

Query: 392 PVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIAN 451
            V +E FAPI+ +++  DFD  L   N    GL  SIFT D+  ++R  A +  D G   
Sbjct: 371 IVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKR--AINELDAGGIV 428

Query: 452 VN-IGTSGAEIGGAFGGEKETGGGRE 476
           +N + T   +I   +GG K +G GRE
Sbjct: 429 INDMPTLRFDI-QPYGGVKLSGVGRE 453


Lambda     K      H
   0.317    0.134    0.390 

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: 21
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: 510
Length of database: 471
Length adjustment: 34
Effective length of query: 476
Effective length of database: 437
Effective search space:   208012
Effective search space used:   208012
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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