GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sedimenticola selenatireducens DSM 17993

Align Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial; SBCAD; 2-methyl branched chain acyl-CoA dehydrogenase; 2-MEBCAD; 2-methylbutyryl-coenzyme A dehydrogenase; 2-methylbutyryl-CoA dehydrogenase; EC 1.3.8.5 (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase

Query= SwissProt::P45954
         (432 letters)



>NCBI__GCF_000428045.1:WP_029134232.1
          Length = 397

 Score =  176 bits (446), Expect = 1e-48
 Identities = 114/366 (31%), Positives = 191/366 (52%), Gaps = 7/366 (1%)

Query: 55  QTFTDEEMMIKSSVKKFAQEQIAPLVSTMDENSKMEKSVIQGLFQQGLMGIEVDPEYGGT 114
           Q  T+EE M++ + +K+ QEQ+ P V   + +   ++ ++  + + GL+G+ +D  Y   
Sbjct: 21  QQLTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTIDG-YDCA 79

Query: 115 GASFLSTVLVIEELAKVDASVAVFCEIQNTLINTLIRKHGTEEQKATYLPQLTT-EKVGS 173
           G +++S  L+  E+ +VD+       +Q++L+   I  +GTEEQ+  YLP+L T E VG 
Sbjct: 80  GLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGC 139

Query: 174 FCLSEAGAGSDSFALKTRADKEGDYYVLNGSKMWISSAEHAGLFLVMANVDPTIGYKGIT 233
           F L+E   GSD   +KTRA      Y L+GSKMWI+++  A +F+V A  D  +    I 
Sbjct: 140 FGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDDEGV----IR 195

Query: 234 SFLVDRDTPGLHIGKPENKLGLRASSTCPLTFENVKVPEANILGQIGHGYKYAIGSLNEG 293
            F++++   GL   K E K  LRAS T  +  + V VP  N+L  +  G     G LN  
Sbjct: 196 GFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNV-KGLAGPFGCLNRA 254

Query: 294 RIGIAAQMLGLAQGCFDYTIPYIKERIQFGKRLFDFQGLQHQVAHVATQLEAARLLTYNA 353
           R GIA  +LG A+ C+   + Y  +R QFG+ L   Q +Q ++A++ T++          
Sbjct: 255 RYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCLQL 314

Query: 354 ARLLEAGKPFIKEASMAKYYASEIAGQTTSKCIEWMGGVGYTKDYPVEKYFRDAKIGTIY 413
            RL +AG+   +  S+ K   +  A        +  GG G + ++ V ++  + +    Y
Sbjct: 315 GRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVNTY 374

Query: 414 EGASNI 419
           EG  ++
Sbjct: 375 EGTHDV 380


Lambda     K      H
   0.318    0.134    0.385 

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: 341
Number of extensions: 16
Number of successful extensions: 5
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: 432
Length of database: 397
Length adjustment: 31
Effective length of query: 401
Effective length of database: 366
Effective search space:   146766
Effective search space used:   146766
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: 41 (21.7 bits)
S2: 50 (23.9 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