GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Sinorhizobium meliloti 1021

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate SMc04405 SMc04405 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Smeli:SMc04405
          Length = 370

 Score =  165 bits (417), Expect = 2e-45
 Identities = 129/364 (35%), Positives = 188/364 (51%), Gaps = 39/364 (10%)

Query: 7   LIEGDGIGHEVIPAARRVLEATGLPLE--FVEAEA--GWETFERRGTSVPEETVEKILSC 62
           L+ GDGIG E +   R+++       +  FV  E   G   ++  G ++ E  + K L+ 
Sbjct: 8   LLPGDGIGPEAMAEVRKIIAYMNAERDAGFVTDEGLVGGSAYDAHGAAISEGDMAKALAA 67

Query: 63  HATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV--------PGSR 109
            A LFGA   P       +V    G +R LR+ L+L+AN+RPA   P         P   
Sbjct: 68  DAVLFGAVGGPKWDAVPYEVRPEAGLLR-LRKDLELFANLRPAICYPALANASSLKPELV 126

Query: 110 PGVDLVIVRENTEGLYVEQERRYLDVA------IADAVISKKASERIGRAALRIAEGRPR 163
            G+D++IVRE T G+Y  + +  +D+       I   V      ERI   A  +A  R  
Sbjct: 127 EGLDILIVRELTGGVYFGEPKEIVDLGNGQKRGIDTQVYDTYEIERIAGVAFELARTRNN 186

Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAK-DFPLVNVQDIIVDNCAMQLVMRPERFDVIVT 222
           +   +  K NV+  +  L+   V E  K  +  V ++ ++ D   MQLV +P++FDVIVT
Sbjct: 187 RVCSM-EKRNVMK-SGVLWNQVVTETHKAKYSDVQLEHMLADAGGMQLVRQPKQFDVIVT 244

Query: 223 TNLLGDILSDLAAGLVGGLGLAPSGNI-------GDTTAVFEPVHGSAPDIAGKGIANPT 275
            NL GD+LSD+AA L G LG+ PS ++       G   A++EPVHGSAPDIAG G+ANP 
Sbjct: 245 DNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKALYEPVHGSAPDIAGTGVANPI 304

Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFT----EAVVEA 330
           A I S AM L Y     + A  +EKA+  VL++G RT D+  +   +  T    +A++  
Sbjct: 305 AMIASFAMCLRYSFNLVKEADDLEKAIANVLDQGIRTGDIMAEGCRKVGTAEMGDAILAE 364

Query: 331 LKSL 334
            KSL
Sbjct: 365 FKSL 368


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: 292
Number of extensions: 16
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: 370
Length adjustment: 29
Effective length of query: 305
Effective length of database: 341
Effective search space:   104005
Effective search space used:   104005
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