GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Azorhizobium caulinodans ORS 571

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_012173167.1 AZC_RS23810 acyl-CoA dehydrogenase family protein

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>NCBI__GCF_000010525.1:WP_012173167.1
          Length = 564

 Score =  214 bits (544), Expect = 6e-60
 Identities = 132/384 (34%), Positives = 207/384 (53%), Gaps = 15/384 (3%)

Query: 5   DEQLQ-ISDAARQFAQERLKPFAAEWDREHRF-PKEAIGEMAELGFFGMLVPEQWGGCDT 62
           DE L+ +    R+F +  + P A EW  ++ + P E IG +AELG FG+ +PE++GG   
Sbjct: 177 DETLEAMRSEIRRFVEAEVVPHAHEWHLKNAYIPLEVIGRLAELGVFGLTIPEEYGGLGL 236

Query: 63  GYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFA 122
              A  +  EE++ G     ++    + +    I+  G D+QK  +L  LASG +L    
Sbjct: 237 PKEAMCVVTEELSRGYIGVGSL-GTRSEIAAELIIGGGTDEQKAHYLPKLASGEILPTAV 295

Query: 123 LTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSA-GKRGISA 181
            TEP  GSD +SL+TRA   GD Y ++G K +IT    A ++ +   T+P+  G +G+S 
Sbjct: 296 FTEPNTGSDLASLRTRAVKEGDVYKVSGNKTWITHPVRADLMTLLVRTNPAEPGYKGLSM 355

Query: 182 FIV---------PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYK 231
            +          P  + G     +E  LG       +I F+  +VP    LG  EG+G+K
Sbjct: 356 LLAEKPRGTDEDPFPAKGMTGGEIE-VLGYRGMKEFEIGFDGFEVPAGQLLGGVEGQGFK 414

Query: 232 IALANLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIA 291
             +   E  R+  A+++VG+A+AA E    YA ER  FGKP+I    VA ++  MA +IA
Sbjct: 415 QLMNTFEAARIQTAARAVGVAQAAMETGLRYAEERIQFGKPLIAFPRVADKIVMMAVEIA 474

Query: 292 VARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIY 351
           +ARQ+ ++AA  +D G+   +EA M+KL  + +A      ALQ  GG G+  ++ + R+ 
Sbjct: 475 IARQITYFAARAKDEGRRTDLEAGMSKLLGARVAWAAADNALQIHGGNGFALEYQVSRLL 534

Query: 352 RDVRVCQIYEGTSDIQRMVISRNL 375
            D R+  I+EG ++IQ  VI+R L
Sbjct: 535 CDARILNIFEGAAEIQAQVIARRL 558



 Score = 29.6 bits (65), Expect = 2e-04
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 4/89 (4%)

Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIE----HQAVAFRLADMATQIAVARQMVHY 299
           + S    + RA  +A +    +  S GK   E     Q     LA +AT +   R+++HY
Sbjct: 21  VRSALPALERALTDATQAVREKVSSGGKLSAELLESEQRAVHGLAWLATYVFGVRELLHY 80

Query: 300 AAALRDSGKPALVEASMAKLFASEMAEKV 328
           A  L  SGK    E  + ++ A E   ++
Sbjct: 81  ADRLGASGKFGEAERLIVQIGAGEYIAQI 109


Lambda     K      H
   0.319    0.134    0.389 

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: 454
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 564
Length adjustment: 33
Effective length of query: 342
Effective length of database: 531
Effective search space:   181602
Effective search space used:   181602
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 (21.8 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