GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Amycolatopsis halophila YIM 93223

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_034274815.1 AMYHA_RS24060 acyl-CoA dehydrogenase family protein

Query= reanno::pseudo5_N2C3_1:AO356_26355
         (375 letters)



>NCBI__GCF_000504245.1:WP_034274815.1
          Length = 393

 Score =  312 bits (800), Expect = 9e-90
 Identities = 161/372 (43%), Positives = 232/372 (62%), Gaps = 1/372 (0%)

Query: 4   TEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTG 63
           T+EQ  ++ +AR F    + P  AEWDR  +     + ++AELGF G+ VPE++GG    
Sbjct: 17  TDEQRAVQQLARDFVDREVVPNVAEWDRAEQVDIGIVKQLAELGFLGLTVPEEYGGSGGD 76

Query: 64  YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123
           +L+Y + +EE   GD A   I+SV   +    I+K+G +EQK  ++  L SG  L  F L
Sbjct: 77  HLSYCLIMEEFGRGDTAIRGIVSVSLGLVTKQIVKYGTEEQKRHWVPRLCSGESLACFGL 136

Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183
           TEP  GSDA +L TRA  +GD +++ G K FIT+G  A V ++FA TD   G +G++AF+
Sbjct: 137 TEPGTGSDAGNLTTRAEQDGDDWIITGQKMFITNGTWADVALIFARTD-GPGPKGVTAFL 195

Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLGEEGEGYKIALANLEGGRVG 243
            PTD+ G+S   ++ KLG     T ++  + V+VP   RLGE G+G+ IA+  L+ GR+ 
Sbjct: 196 APTDAEGFSRTEIKGKLGLRGQATAELTLDGVRVPDSARLGERGQGFSIAMFALDKGRMA 255

Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303
           +AA  VG+ARAA EA+  YA+ER  FGKPI   Q V   LADMA +   AR +V   A  
Sbjct: 256 VAAGCVGLARAALEASVKYAKEREQFGKPIASFQLVQEMLADMAVETDAARLLVWRVADY 315

Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363
            + G     EASMAKL+ASE A K  ++A+Q  GGYGY++++P+ +  RD RV  +YEGT
Sbjct: 316 IERGLTFKTEASMAKLYASEAAVKASNLAIQVFGGYGYIDEYPVSKFLRDARVLTLYEGT 375

Query: 364 SDIQRMVISRNL 375
           + IQ+++I R+L
Sbjct: 376 TQIQKLLIGRSL 387


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: 348
Number of extensions: 16
Number of successful extensions: 2
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: 393
Length adjustment: 30
Effective length of query: 345
Effective length of database: 363
Effective search space:   125235
Effective search space used:   125235
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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