GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Sedimenticola selenatireducens DSM 17993

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase

Query= BRENDA::P26440
         (426 letters)



>NCBI__GCF_000428045.1:WP_029134232.1
          Length = 397

 Score =  199 bits (506), Expect = 1e-55
 Identities = 126/376 (33%), Positives = 192/376 (51%), Gaps = 10/376 (2%)

Query: 45  LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGS 104
           L+EE+R +R T  K+ QE L P+  E +R   F   RE   ++G LG+LG+T    Y  +
Sbjct: 23  LTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFD--REIMNEMGELGLLGVTID-GYDCA 79

Query: 105 GLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGA 164
           GL Y+ + L+  E+ R       +    S+L ++ +   G E Q+EKYLPKL +GE +G 
Sbjct: 80  GLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGC 139

Query: 165 LAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRG 224
             ++EP+ GSD   MK +A      Y L+G+K WITN P ADV IV+AK D         
Sbjct: 140 FGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDDEGV------ 193

Query: 225 ITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSGLD 284
           I  FI+EKGM G S  K   K  +R S T E++ ++  +PA N+L +  KG+      L+
Sbjct: 194 IRGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNV-KGLAGPFGCLN 252

Query: 285 LERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQYVY 344
             R  +A G LG  +      + Y   R+ FG+ +   QL+Q K+A+M T +    Q   
Sbjct: 253 RARYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCL 312

Query: 345 NVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDAKLYE 404
            + +  D G    +  + +   +A  A  +A       GGNG  ++F + R   + +   
Sbjct: 313 QLGRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVN 372

Query: 405 IGAGTSEVRRLVIGRA 420
              GT +V  L++GRA
Sbjct: 373 TYEGTHDVHALILGRA 388


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: 407
Number of extensions: 26
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: 397
Length adjustment: 31
Effective length of query: 395
Effective length of database: 366
Effective search space:   144570
Effective search space used:   144570
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 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