GapMind for Amino acid biosynthesis

 

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

Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate N515DRAFT_1138 N515DRAFT_1138 isocitrate dehydrogenase (NAD+)

Query= BRENDA::P50213
         (366 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1138
          Length = 338

 Score =  307 bits (787), Expect = 2e-88
 Identities = 164/337 (48%), Positives = 224/337 (66%), Gaps = 8/337 (2%)

Query: 32  QTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWE--ERNVTAIQGPGGKWMIPSEAKESMD 89
           +T+ +IPGDGIGPEI  A +++ DA    + +E  +  + A++  G   ++P +  +++ 
Sbjct: 3   KTIAVIPGDGIGPEIMKATLRVLDALDCGLSYEFVDAGMVALEKHGD--LLPKDTLDAIA 60

Query: 90  KNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENT 149
           ++ + LKGPL TPI  G  S+N+ LR+ FDLYANVRP +S  G K  + +++I+T+RENT
Sbjct: 61  RHTIALKGPLTTPIGGGFTSINVTLRRHFDLYANVRPAISFPGTKARFENIDIITVRENT 120

Query: 150 EGEY-SGIEHVIVDG-VVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMS 207
           EG Y S  + +  DG V  S+   T   S RI ++AFE AR   R  +TAVHKANIM+ S
Sbjct: 121 EGAYLSEGQTLSEDGEVATSMVRNTRKGSTRIVKYAFEMARQKGRKKITAVHKANIMKTS 180

Query: 208 DGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLI 267
            GLFL   REVA+   DI+FNEM +D  C+ +V  P QFDV+V  NL+GDILSDLCAGL+
Sbjct: 181 SGLFLNVAREVAKEYPDIEFNEMIVDNTCMQLVMKPEQFDVIVTTNLFGDILSDLCAGLV 240

Query: 268 GGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARI 327
           GGLG+ P  NIGA G AIFE+VHG+APDIAGK +ANP ALLL+A  ML H+G+ D   ++
Sbjct: 241 GGLGLAPGDNIGA-GAAIFEAVHGSAPDIAGKGIANPCALLLAAADMLDHLGMADKGNKV 299

Query: 328 EAACFATI-KDGKSLTKDLGGNAKCSDFTEEICRRVK 363
            AA   T+  D  ++T DLGG      F + I +RVK
Sbjct: 300 RAAIRDTLTNDRDAVTPDLGGKGNTDSFGDAIVKRVK 336


Lambda     K      H
   0.319    0.136    0.403 

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: 348
Number of extensions: 17
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: 366
Length of database: 338
Length adjustment: 29
Effective length of query: 337
Effective length of database: 309
Effective search space:   104133
Effective search space used:   104133
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