GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Rhodobacter viridis JA737

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_110806794.1 C8J30_RS15730 acyl-CoA/acyl-ACP dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1146
         (375 letters)



>NCBI__GCF_003217355.1:WP_110806794.1
          Length = 547

 Score =  229 bits (583), Expect = 2e-64
 Identities = 142/383 (37%), Positives = 209/383 (54%), Gaps = 14/383 (3%)

Query: 5   EEQTQIRDMARQFAEERLKPFAAEWD-REHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63
           EE   IR+   ++AEER+ P A EW  ++   P E I+E+A+LG FG+ +PE++GG    
Sbjct: 165 EELEMIREQFHRYAEERVIPNAHEWHLKDELIPMEIIEELADLGVFGLTIPEEYGGLGLS 224

Query: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
             +  +  EE++ G     ++    + +    IL  G +EQK K+L  LASG +L     
Sbjct: 225 KASMVVVTEELSRGYIGVGSL-GTRSEIAAELILCGGTEEQKQKWLPGLASGQILSTAVF 283

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGK-RGISAF 182
           TEP  GSD  SL+TRA  EGD +V+ G K +IT  Q   V+ + A T+P     RG+S F
Sbjct: 284 TEPNTGSDLGSLRTRAVKEGDDWVITGNKTWITHAQRTHVMTLLARTEPDTTDWRGLSMF 343

Query: 183 IV---------PTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLG-EEGEGYKI 232
           +          P  +PG +   +E  LG       ++ F+  +V   N LG E G G+K 
Sbjct: 344 LAEKTPGTDENPFPTPGMTGGEIE-VLGYRGMKEYELGFDGFRVKGENLLGGETGRGFKQ 402

Query: 233 ALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAV 292
            +   E  R+  AA+AVG+A+AA E    YA +R  FGK +IE   V  +LA MA +I +
Sbjct: 403 LMETFESARIQTAARAVGVAQAACEIGMRYAIDRKQFGKSLIEFPRVGGKLAMMAVEIMI 462

Query: 293 ARQMVHYAAALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYR 352
           ARQ+ +++A  +D G    VEA MAKL  + +A      ALQ  GG G+  ++ + RI  
Sbjct: 463 ARQLTYFSAWEKDHGHRCDVEAGMAKLLGARVAWAASDNALQIHGGNGFALEYTISRILC 522

Query: 353 DVRVCQIYEGTSDIQRMVISRNL 375
           D R+  I+EG ++IQ  VI+R L
Sbjct: 523 DARILNIFEGAAEIQAQVIARRL 545


Lambda     K      H
   0.320    0.134    0.388 

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: 449
Number of extensions: 24
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: 375
Length of database: 547
Length adjustment: 33
Effective length of query: 342
Effective length of database: 514
Effective search space:   175788
Effective search space used:   175788
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 Sep 24 2021. 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