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

GapMind for Amino acid biosynthesis

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_1138
          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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources, 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

GapMind for Amino acid biosynthesis