GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Methylotuvimicrobium alcaliphilum 20Z

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_014148950.1 MEALZ_RS12210 prephenate dehydrogenase/arogenate dehydrogenase family protein

Query= uniprot:D8IR44_HERSS
         (295 letters)



>NCBI__GCF_000968535.2:WP_014148950.1
          Length = 291

 Score =  219 bits (557), Expect = 8e-62
 Identities = 117/285 (41%), Positives = 165/285 (57%), Gaps = 2/285 (0%)

Query: 1   MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRS--LQSLERARELGIIDAVATDAAS 58
           MF K+ + GVGLIGGS A A R  G    IV  GR   L +L+ AR LG+ID    +  +
Sbjct: 1   MFNKLCLIGVGLIGGSIARAARDRGLCTTIVAYGREIDLDNLKEARRLGVIDEYFINLEA 60

Query: 59  AVQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFI 118
           AVQGAD I++A PV     +L  + P+   QA+ +D GSTK +VV AAR   G     F+
Sbjct: 61  AVQGADCIIIATPVGAIEKVLGELKPYWSEQAVYSDVGSTKGNVVDAARRVFGYLPSNFV 120

Query: 119 PAHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQE 178
           PAHPIAG E+ G  A++  L++ K+++IT + + D      +   W+  GA++  +    
Sbjct: 121 PAHPIAGAEQSGVTASVNGLFDDKRLIITPVEQTDPKATATMQQFWQQLGAIVSIMEVDH 180

Query: 179 HDAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLA 238
           HDAV A+ SHLPH+LAF LVD +  K     +F+YAA GF+DFTRIA+S P MW DI LA
Sbjct: 181 HDAVLAATSHLPHLLAFVLVDLLGRKDEQVEIFKYAAGGFKDFTRIASSDPTMWLDICLA 240

Query: 239 NRDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283
           N+  L+  +     +L  +   +   D   I + +  A  ARQ++
Sbjct: 241 NKQKLIPLIQQLKQELDTMELALENDDSQQIFQTFTYAGQARQRF 285


Lambda     K      H
   0.320    0.132    0.376 

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: 189
Number of extensions: 11
Number of successful extensions: 2
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: 295
Length of database: 291
Length adjustment: 26
Effective length of query: 269
Effective length of database: 265
Effective search space:    71285
Effective search space used:    71285
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 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Jul 25 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