GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Ruegeria conchae TW15

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase

Query= BRENDA::P26440
         (426 letters)



>NCBI__GCF_000192475.1:WP_010441027.1
          Length = 385

 Score =  236 bits (603), Expect = 7e-67
 Identities = 138/381 (36%), Positives = 216/381 (56%), Gaps = 10/381 (2%)

Query: 45  LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGS 104
           +++E R   +   +F+ + L P  ++          R+FW Q G  G++  +   +YGG 
Sbjct: 11  VTDEHRMFAEMAGRFMDDALVPNTEKWAEDGVVD--RDFWLQAGQTGLMAGSIAEEYGGV 68

Query: 105 GLGY-LEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIG 163
           G G   + V + E+ +R  G  G  YG  S +  + +   G+E QK K+LPKL SGE IG
Sbjct: 69  GGGMGFDSVTLYEQTAR--GDAGWGYGIQS-IVTHYITTYGSEDQKHKWLPKLASGEMIG 125

Query: 164 ALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASR 223
           ALAM+EP  GSDV ++K  AEK GN Y L G+K +ITNG  AD++IV AKTD +    ++
Sbjct: 126 ALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL--GAK 183

Query: 224 GITAFIVE-KGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILG-HENKGVYVLMS 281
           G++   VE +G  GF   + L+KLGM+G++T EL FED K+P  N+LG  E +G Y LM 
Sbjct: 184 GVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMK 243

Query: 282 GLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQ 341
            L  ERL +    LG +   +  T+ Y+  R+AFGQ++  FQ  + K+A+  T+    R 
Sbjct: 244 QLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRS 303

Query: 342 YVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDAK 401
           +V +     + G   A   + V  + +E   ++  + +Q FGG G++ ++P+ R   DA+
Sbjct: 304 FVNDCIGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADAR 363

Query: 402 LYEIGAGTSEVRRLVIGRAFN 422
           +  I  GT+EV + +I R+ +
Sbjct: 364 VQMIYGGTNEVMKELIARSLD 384


Lambda     K      H
   0.321    0.137    0.410 

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: 392
Number of extensions: 22
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: 426
Length of database: 385
Length adjustment: 31
Effective length of query: 395
Effective length of database: 354
Effective search space:   139830
Effective search space used:   139830
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