GapMind for catabolism of small carbon sources

 

Aligments for a candidate for icd in Desulfovibrio vulgaris Miyazaki F

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 8501058 DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::Q5SIJ1
         (334 letters)



>lcl|FitnessBrowser__Miya:8501058 DvMF_1794 3-isopropylmalate
           dehydrogenase (RefSeq)
          Length = 358

 Score =  195 bits (495), Expect = 2e-54
 Identities = 135/349 (38%), Positives = 189/349 (54%), Gaps = 35/349 (10%)

Query: 1   MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56
           M  +ICL+ GDGIG E++  A +VL+      G  + +  A  G    +  G  +P+ETV
Sbjct: 1   MDMKICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETV 60

Query: 57  EKILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPG- 107
               +  A L GA   P         R   G  G    +R+ L L+AN+RPA   P    
Sbjct: 61  AACKAADAVLLGAVGGPKWDTLPTAIRPEKGLLG----IRKALGLFANLRPATLLPELAG 116

Query: 108 --------SRPGVDLVIVRENTEGLYV------EQERRYLDVAIADAVISKKASERIGRA 153
                   +  G+D+++VRE T G+Y       E+ R  L  +    + +++   RI R 
Sbjct: 117 ACLLRADIAAQGLDVMVVRELTGGVYFGEPVCEEELRDGLRTSYNTMIYNEEEVRRIARV 176

Query: 154 ALRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMR 213
           A   A  R RK   +  KANVL +++ L+   V EVA+++P V +  + VDN AMQLV  
Sbjct: 177 AFEAARKRSRKVCSV-DKANVLAVSR-LWRAVVIEVAREYPDVELTHMYVDNAAMQLVRW 234

Query: 214 PERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNIGDT-TAVFEPVHGSAPDIAGKGIA 272
           P +FDVIVT NL GDILSD AA + G +G+ PS ++G +   +FEP+HGSAPDIAG+  A
Sbjct: 235 PAQFDVIVTENLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKA 294

Query: 273 NPTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATT 320
           NP A ILS AMML Y  G ++ A  +E+AV  VL  G RT D+  +  T
Sbjct: 295 NPVATILSVAMMLRYTFGLEKEAVAIEQAVSGVLREGYRTGDIMEEGKT 343


Lambda     K      H
   0.319    0.137    0.391 

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: 317
Number of extensions: 19
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: 334
Length of database: 358
Length adjustment: 29
Effective length of query: 305
Effective length of database: 329
Effective search space:   100345
Effective search space used:   100345
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 (21.7 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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