GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Epibacterium ulvae U95

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_090219233.1 CV091_RS13570 isocitrate/isopropylmalate dehydrogenase family protein

Query= BRENDA::Q4JB37
         (337 letters)



>NCBI__GCF_002796795.1:WP_090219233.1
          Length = 357

 Score =  203 bits (516), Expect = 6e-57
 Identities = 123/337 (36%), Positives = 196/337 (58%), Gaps = 20/337 (5%)

Query: 11  DGIGPEVVSKSKTILARLNEKFSLPIEYIEVEAGDTTKNKFGDALPKDSL-RVIEKADMI 69
           DGIGPE+++++  ++   N KF L + + E E+G  +  K+G  L ++ L R   + D +
Sbjct: 9   DGIGPEIMAETLRVVEAANHKFDLGLTFHEEESGFKSLEKYGITLREEVLDRARTEFDGV 68

Query: 70  LKG--------PVGETAADVVVKLRLMYDLYANLRPAKSLPGLENKFGDVDILVVRENTE 121
           + G        P+ E   +V    R+  DLYAN+RPA++   + NK  D+D++++RE TE
Sbjct: 69  ILGTQSHMDYPPLVEGGRNVSAGFRIGLDLYANVRPARTRDFIPNKAPDMDLVIMREATE 128

Query: 122 ------DLYKGLEHVISD-GVTVGIKVITRAASTRIAQVALNQALRRKKKVVCVHKSNVM 174
                 ++Y+G+  ++ D  + + ++ ITR  S RI +     A++RKKK+  +HK+N  
Sbjct: 129 GFYPDRNMYQGVGEMMPDPNMALSVRKITREGSLRICREGFKLAMQRKKKIAAIHKANSF 188

Query: 175 RITDGLFAESCRNVLKG--KVEYSEMYVDAAAANLVRNPQAFDVIVTENTYGDILSDEAG 232
            +TDGLF E  R V K   +V+  E+ VDA AA LVR P+A+DV+V  N YGDILSD A 
Sbjct: 189 LMTDGLFLECFREVAKDFPEVQTEELIVDAFAALLVRKPEAYDVVVATNFYGDILSDLAS 248

Query: 233 QIAGSLGISPSANIGDRKSL--FEPVHGAAFDIAGKNIANPTAFLLSVGMMLDRMQELSG 290
           +++GSLG++ S N      L   +  HG+A DI G N+ANPT+ +LS  MML  + E  G
Sbjct: 249 ELSGSLGLAGSINANAETGLCCAQAQHGSAPDIQGLNVANPTSLILSAAMMLTWLGEQRG 308

Query: 291 DIRYNNAAKSLRDAIYSVYSEGKYLTPDVGGSSTTDE 327
             +  +A  ++  A+ +V  +    T D+GG+   D+
Sbjct: 309 IQKLQDAGHAIAAAVDAVIDDPAKRTRDLGGTVNCDD 345


Lambda     K      H
   0.316    0.135    0.369 

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: 266
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: 337
Length of database: 357
Length adjustment: 29
Effective length of query: 308
Effective length of database: 328
Effective search space:   101024
Effective search space used:   101024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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