GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Dinoroseobacter shibae DFL-12

Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= SwissProt::Q9FS87
         (412 letters)



>FitnessBrowser__Dino:3607424
          Length = 382

 Score =  252 bits (643), Expect = 2e-71
 Identities = 144/383 (37%), Positives = 223/383 (58%), Gaps = 5/383 (1%)

Query: 29  STSLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPE 88
           S++    D  +   E    F     APH E+    +    D  +W+  G   LL  +VPE
Sbjct: 2   SSTTWMTDEHRMLAEMTRNFITTEWAPHFERW--RDQGEMDREIWQQAGELGLLCPSVPE 59

Query: 89  EYGGLGLGYLYHCIAMEEISRASGSV-GLSYGAHTNLCINQLVRNGTHEQKQKYLPKLIS 147
            YGG G  + +    + EI+RA+ S  G  +G H+ +  + ++  G+ EQKQK+LPK++S
Sbjct: 60  AYGGPGGDFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVS 119

Query: 148 GEHVGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTA 207
           GE VGALAM+EP AGSD+  +K +A +   GY L+G+K++ TNG  A  +VV AKTD +A
Sbjct: 120 GEMVGALAMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSA 179

Query: 208 GSKGITAFIIE-KGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVL-GQVGRGVYV 265
           G+KG++  ++E +G  GFS  + L K+GM  SDT EL F+N  +P EN+L G+VG+G Y 
Sbjct: 180 GAKGVSLVVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQ 239

Query: 266 LMSGLDLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQS 325
           +M+ L  ERL++A+G VG M+  ++  + Y K+R+ FG PI +FQ  + K+A+  T    
Sbjct: 240 MMTQLPQERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTV 299

Query: 326 SRSYLYSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLR 385
           +R++L     E   G ++ +  A       +   +V  + +Q  GG GY+ EY   +   
Sbjct: 300 ARAFLNECMAEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWS 359

Query: 386 DAKLYEIGAGTSEIRRMIIGREL 408
           DA++  I  GT+EI + +IGR L
Sbjct: 360 DARVQRIYGGTNEIMKELIGRAL 382


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: 385
Number of extensions: 21
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: 412
Length of database: 382
Length adjustment: 31
Effective length of query: 381
Effective length of database: 351
Effective search space:   133731
Effective search space used:   133731
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 17 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