GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Trichormus variabilis ATCC 29413

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  254 bits (648), Expect = 6e-72
 Identities = 155/475 (32%), Positives = 250/475 (52%), Gaps = 11/475 (2%)

Query: 7   INGELVSGEGEKQ-PVYNPAT-GDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64
           ING+ ++   E     +NPA   +++     + A+  D AV AA  A+  W +     RA
Sbjct: 11  INGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAPARA 70

Query: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124
           E + ++ +++ ++ +  A+L SR  GKP+  A  D +   VD   + AG  R L G    
Sbjct: 71  EYIFRVGELLLQHKEELAQLISREMGKPITEARGD-VQEGVDCAFYSAGEGRRLFGQTTP 129

Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184
             +    +M  R P+GV A I PWN+P+ +  WK  PAL  GN V+LKP+E TP  A KL
Sbjct: 130 SEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACATKL 189

Query: 185 AEL-AKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243
            E+ A    P GVIN++ G G+  G  L  HP + +VS TGS ATG ++      + KR 
Sbjct: 190 IEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHKRV 249

Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303
            +E+GGK   +V +DAD+E  ++G     +   GQ CTA  R+   + I +     L   
Sbjct: 250 CLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLRER 309

Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG----EKRKGNGYY 359
            + L+ GA  +  T++GP+ +   L+RV + +  A+  G  K++ GG    E +   GY+
Sbjct: 310 TSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEG-AKILIGGEIVTEGQLKQGYF 368

Query: 360 YAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAH 419
           + PT+L        + ++E+FGPVV++      E+ +   ND++YGL+SSV+T+D+ RA 
Sbjct: 369 FQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRAF 428

Query: 420 RVSARLQYGCTWVNTHFMLVS-EMPHGGQKLSGYG-KDMSLYGLEDYTVVRHVMV 472
                ++ G T++N   +     +P GG K +G G ++     L+ +T  + V V
Sbjct: 429 VAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSVYV 483


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: 548
Number of extensions: 31
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: 474
Length of database: 498
Length adjustment: 34
Effective length of query: 440
Effective length of database: 464
Effective search space:   204160
Effective search space used:   204160
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