GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Sulfurimonas denitrificans DSM 1251

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000012965.1:WP_011373513.1
          Length = 471

 Score =  197 bits (502), Expect = 5e-55
 Identities = 137/457 (29%), Positives = 227/457 (49%), Gaps = 15/457 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           NP  G+V  E    +A+    A+  A  A  E  +TT   R   LL +A  + +N +  A
Sbjct: 22  NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG--LAAGEYLEGHT--SMIRRDP 138
           +  +   GKP+  +   E+   ++     A   R ++G  +    +  G    S   R P
Sbjct: 82  KTITDEVGKPITYS-RIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140

Query: 139 LGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAEL--AKDIFPAGV 196
            GVV +I P+N+PL + A K+APAL AGN V+LKP+   PLTA K A+L    +      
Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200

Query: 197 INILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF 256
           +++++G    VG  L      R++S TGS+  GE I    ++ IK+  +ELGG A   + 
Sbjct: 201 LSVVYG-DADVGGTLVTSEIPRVISFTGSVGVGEIITK--SAGIKKVSLELGGNAATFID 257

Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316
             A+++   +      + N+GQ C +  RIY  K IY     K+  A   L  G+P +E 
Sbjct: 258 KSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEED 317

Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQ 376
           T +GPL +    +R  + V+ A   G   ++    + +  G  + P ++A   +D AIV 
Sbjct: 318 TFMGPLVNDEAAKRAMEWVQSAIKEGATPIL----EPRVEGRVFYPCVMADVKEDMAIVC 373

Query: 377 KEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHF 436
           +EVF P+VS+    + ++ +   N+S YGL  S++T D+    R    L  G   +N   
Sbjct: 374 QEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMP 433

Query: 437 MLVSEM-PHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472
            L  ++ P+GG KLSG G++   + +E+ + ++ V++
Sbjct: 434 TLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470


Lambda     K      H
   0.317    0.134    0.397 

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: 459
Number of extensions: 32
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: 474
Length of database: 471
Length adjustment: 33
Effective length of query: 441
Effective length of database: 438
Effective search space:   193158
Effective search space used:   193158
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