GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuB in Dyella japonica UNC79MFTsu3.2

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate N515DRAFT_1138 N515DRAFT_1138 isocitrate dehydrogenase (NAD+)

Query= BRENDA::Q5SIJ1
         (334 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1138 N515DRAFT_1138
           isocitrate dehydrogenase (NAD+)
          Length = 338

 Score =  280 bits (715), Expect = 5e-80
 Identities = 160/340 (47%), Positives = 220/340 (64%), Gaps = 10/340 (2%)

Query: 1   MAYRICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKIL 60
           M+  I +I GDGIG E++ A  RVL+A    L +   +AG    E+ G  +P++T++ I 
Sbjct: 1   MSKTIAVIPGDGIGPEIMKATLRVLDALDCGLSYEFVDAGMVALEKHGDLLPKDTLDAIA 60

Query: 61  SCHATLFGAATSPTRKVPGFFGAIRY-LRRRLDLYANVRPAKSRPVPGSR-PGVDLVIVR 118
                L G  T+P   + G F +I   LRR  DLYANVRPA S P   +R   +D++ VR
Sbjct: 61  RHTIALKGPLTTP---IGGGFTSINVTLRRHFDLYANVRPAISFPGTKARFENIDIITVR 117

Query: 119 ENTEGLYVEQERRYL-DVAIADAVI--SKKASERIGRAALRIAEGRPRKTLHIAHKANVL 175
           ENTEG Y+ + +    D  +A +++  ++K S RI + A  +A  + RK +   HKAN++
Sbjct: 118 ENTEGAYLSEGQTLSEDGEVATSMVRNTRKGSTRIVKYAFEMARQKGRKKITAVHKANIM 177

Query: 176 PLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTNLLGDILSDLAA 235
             + GLFL+  +EVAK++P +   ++IVDN  MQLVM+PE+FDVIVTTNL GDILSDL A
Sbjct: 178 KTSSGLFLNVAREVAKEYPDIEFNEMIVDNTCMQLVMKPEQFDVIVTTNLFGDILSDLCA 237

Query: 236 GLVGGLGLAPSGNIGDTTAVFEPVHGSAPDIAGKGIANPTAAILSAAMMLDYLGEKEAAK 295
           GLVGGLGLAP  NIG   A+FE VHGSAPDIAGKGIANP A +L+AA MLD+LG  +   
Sbjct: 238 GLVGGLGLAPGDNIGAGAAIFEAVHGSAPDIAGKGIANPCALLLAAADMLDHLGMADKGN 297

Query: 296 RVEKAV--DLVLERGPRTPDLGGDATTEAFTEAVVEALKS 333
           +V  A+   L  +R   TPDLGG   T++F +A+V+ +K+
Sbjct: 298 KVRAAIRDTLTNDRDAVTPDLGGKGNTDSFGDAIVKRVKA 337


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: 289
Number of extensions: 13
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: 338
Length adjustment: 28
Effective length of query: 306
Effective length of database: 310
Effective search space:    94860
Effective search space used:    94860
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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