GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Pontibacillus litoralis JSM 072002

Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase

Query= SwissProt::Q9FS87
         (412 letters)



>NCBI__GCF_000775615.1:WP_036834462.1
          Length = 379

 Score =  322 bits (825), Expect = 1e-92
 Identities = 163/380 (42%), Positives = 247/380 (65%), Gaps = 2/380 (0%)

Query: 31  SLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEY 90
           +L F + Q   ++ V  FA + +AP  +++D+ +YFP  + L K MG+  L+GI +PE+Y
Sbjct: 2   NLQFTEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFP--IELIKQMGDIGLMGIPIPEQY 59

Query: 91  GGLGLGYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEH 150
           GG G+ +  + IA+ E+S+ S SVG+    HT++  N ++  GT EQKQKY+PKL SGE 
Sbjct: 60  GGSGMDFPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEF 119

Query: 151 VGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSK 210
           +GA A++EP AGSD  S+K KA R    Y+LNG+K++ TNG  A T +V+A+TD  AG+K
Sbjct: 120 LGAFALTEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNK 179

Query: 211 GITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLMSGL 270
           G+TAFI+E+  +GF   +K  K+GM GS T  L F+NC +P E  LG+ G G  + M+ L
Sbjct: 180 GVTAFIVERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANL 239

Query: 271 DLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSRSYL 330
           ++ R+ +A+  +GI +A L+  + Y K+REQFG+PI   Q +  K+ADM TS+++++   
Sbjct: 240 NVGRIGIAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLT 299

Query: 331 YSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDAKLY 390
           Y  A     G    K+ +   ++A++ A  VA +AIQ  GG GY  +YP  RF RDAK+ 
Sbjct: 300 YHAANLRHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVC 359

Query: 391 EIGAGTSEIRRMIIGRELFK 410
           EI  GT+EI+R++IG+ + K
Sbjct: 360 EIYEGTNEIQRVVIGKHVLK 379


Lambda     K      H
   0.319    0.135    0.396 

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: 384
Number of extensions: 24
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: 412
Length of database: 379
Length adjustment: 31
Effective length of query: 381
Effective length of database: 348
Effective search space:   132588
Effective search space used:   132588
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.

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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