GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Epibacterium ulvae U95

Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate WP_090215785.1 CV091_RS06950 prephenate/arogenate dehydrogenase family protein

Query= uniprot:Q92MG1
         (307 letters)



>NCBI__GCF_002796795.1:WP_090215785.1
          Length = 306

 Score =  373 bits (958), Expect = e-108
 Identities = 191/300 (63%), Positives = 224/300 (74%)

Query: 2   AQQFQTIALIGIGLIGSSIARDIREKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAE 61
           A  +  IALIG+GLI SS+   I+   LA  +    +S  +   A  +GL DR   SAAE
Sbjct: 3   APVYDRIALIGLGLIASSMYWAIKRAGLAQEVTGFAKSAESRATARRIGLCDRVCESAAE 62

Query: 62  AVEGADLVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVP 121
           AVEGADLVV+ VPVGA G VAAEIA HLK GA V+DVGS K SV+ Q+ PHLP+ VHFVP
Sbjct: 63  AVEGADLVVLCVPVGAMGRVAAEIAPHLKVGATVSDVGSVKRSVVEQVGPHLPEGVHFVP 122

Query: 122 GHPIAGTEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHH 181
            HPIAGTEHSGP++GFA LF  RWC+L P  GTD EAV  LR  WE +G+ VDEM   HH
Sbjct: 123 AHPIAGTEHSGPESGFATLFDNRWCLLVPVEGTDPEAVQCLRTLWEGMGAKVDEMTADHH 182

Query: 182 DKVLAIVSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCL 241
           D VLA+ SH PH+IAY +VG ADDL+ VT+ EVI YSA+GFRDFTR+AASDPTMWRDV L
Sbjct: 183 DLVLAVTSHAPHLIAYTMVGVADDLQRVTDGEVINYSAAGFRDFTRIAASDPTMWRDVFL 242

Query: 242 HNKDAILEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIVQAGQDTAMPDFGR 301
            NK+A LE+L RF+E+L +LQRAIR GDGD L + FTRTRAIRR I+ AGQDTA P+FGR
Sbjct: 243 TNKEATLEILGRFTEELFALQRAIRTGDGDHLHEYFTRTRAIRRGIIDAGQDTAAPNFGR 302


Lambda     K      H
   0.320    0.135    0.398 

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: 290
Number of extensions: 7
Number of successful extensions: 1
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: 307
Length of database: 306
Length adjustment: 27
Effective length of query: 280
Effective length of database: 279
Effective search space:    78120
Effective search space used:    78120
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 (21.8 bits)
S2: 48 (23.1 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