GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Methylocystis bryophila S285

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_085772269.1 B1812_RS14765 acyl-CoA dehydrogenase family protein

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



>NCBI__GCF_002117405.1:WP_085772269.1
          Length = 557

 Score =  211 bits (538), Expect = 3e-59
 Identities = 132/387 (34%), Positives = 205/387 (52%), Gaps = 21/387 (5%)

Query: 5   DEQLQ-ISDAARQFAQERLKPFAAEWDREHRF-PKEAIGEMAELGFFGMLVPEQWGGCDT 62
           DE L+ I    R+FA + + PFA EW  ++ + P E I  +AELG FG+ +PE++GG   
Sbjct: 173 DETLEAIRSEMRKFASDNVTPFAQEWHAKNEYIPLEVISGLAELGVFGLTIPEEFGGSGM 232

Query: 63  GYLAYAMALEEIAA---GDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLG 119
           G +A  +  EE++    G G+  T   +   +    IL  G   QKE++L  +A+G +L 
Sbjct: 233 GKIAMCVVSEELSRAYIGVGSLGTRSEIAGEL----ILVGGTKAQKEKYLPKIAAGEILP 288

Query: 120 AFALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSA-GKRG 178
               TEP  GSD + L+TRA   GD Y + G K +IT    A V+ +   T+P   G +G
Sbjct: 289 TAVFTEPNNGSDLAGLRTRAVREGDVYKVTGNKTWITHPVRADVMTLLVRTNPEEKGYKG 348

Query: 179 ISAFIV---------PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGE 228
           +S  +          P  + G     +E  LG       +I F+  + P  N LG  EG 
Sbjct: 349 LSMLLAEKPRGTDENPFPAKGMTGGEIE-VLGYRGMKEFEIGFDGFETPAENLLGGVEGN 407

Query: 229 GYKIALANLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMAT 288
           G+K  +   E  R+  A++++G+A+ A +    YA+ER  FGKP+     +  ++  MA 
Sbjct: 408 GFKQLMETFESARIQTAARALGVAQCALDLGLRYAKERIQFGKPLFSFPRIFDKIVAMAV 467

Query: 289 QIAVARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLE 348
           +I VARQ+ +++A  +D GK   +EA MAKL  + +A      ALQ  GG G+  ++P+ 
Sbjct: 468 EIHVARQITYFSARQKDGGKRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYPVS 527

Query: 349 RIYRDVRVCQIYEGTSDIQRMVISRNL 375
           R+  D R+  I+EG ++IQ  VI+R L
Sbjct: 528 RVLCDARILNIFEGAAEIQAQVIARRL 554


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: 407
Number of extensions: 23
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: 557
Length adjustment: 33
Effective length of query: 342
Effective length of database: 524
Effective search space:   179208
Effective search space used:   179208
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