GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Azorhizobium caulinodans ORS 571

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_012173167.1 AZC_RS23810 acyl-CoA dehydrogenase family protein

Query= BRENDA::Q18AQ1
         (378 letters)



>NCBI__GCF_000010525.1:WP_012173167.1
          Length = 564

 Score =  226 bits (575), Expect = 2e-63
 Identities = 140/373 (37%), Positives = 211/373 (56%), Gaps = 14/373 (3%)

Query: 18  FAENEVKPLATELDEEERF-PYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELS 76
           F E EV P A E   +  + P E + ++A+ G+ G+  P+EYGG G       +  EELS
Sbjct: 190 FVEAEVVPHAHEWHLKNAYIPLEVIGRLAELGVFGLTIPEEYGGLGLPKEAMCVVTEELS 249

Query: 77  RVCGTTGV-ILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASG 135
           R  G  GV  L   + + +  I   G +EQK  +L  LASGE L     TEPN G+D + 
Sbjct: 250 R--GYIGVGSLGTRSEIAAELIIGGGTDEQKAHYLPKLASGEILPTAVFTEPNTGSDLAS 307

Query: 136 QQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSK-GNKGISAFIVEK--GTPGF 192
            +T AV +GD Y ++G+K +IT+ +  D+  ++  T+ ++ G KG+S  + EK  GT   
Sbjct: 308 LRTRAVKEGDVYKVSGNKTWITHPVRADLMTLLVRTNPAEPGYKGLSMLLAEKPRGTDED 367

Query: 193 SFGVKE------KKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGI 245
            F  K       + +G RG    E+ F+   +P   LLG  EGQGFK  M+T +  RI  
Sbjct: 368 PFPAKGMTGGEIEVLGYRGMKEFEIGFDGFEVPAGQLLGGVEGQGFKQLMNTFEAARIQT 427

Query: 246 AAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINK 305
           AA+A+G+AQ A++  ++Y +ER+QFG+PL  F     ++  M V++  AR + Y AA  K
Sbjct: 428 AARAVGVAQAAMETGLRYAEERIQFGKPLIAFPRVADKIVMMAVEIAIARQITYFAARAK 487

Query: 306 DLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTS 365
           D G+   +EA M+KL  A  A      A+Q+HGG G+  +Y V R++ DA+I  I+EG +
Sbjct: 488 DEGRRTDLEAGMSKLLGARVAWAAADNALQIHGGNGFALEYQVSRLLCDARILNIFEGAA 547

Query: 366 EVQRMVISGKLLK 378
           E+Q  VI+ +LL+
Sbjct: 548 EIQAQVIARRLLE 560


Lambda     K      H
   0.315    0.133    0.373 

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: 458
Number of extensions: 18
Number of successful extensions: 3
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: 378
Length of database: 564
Length adjustment: 33
Effective length of query: 345
Effective length of database: 531
Effective search space:   183195
Effective search space used:   183195
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: 42 (22.0 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