GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh 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)



>FitnessBrowser__Miya:8501058
          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 Aug 03 2021. The underlying query database was built on Aug 03 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