GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Pseudomonas putida KT2440

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate PP_1770 PP_1770 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:D8IR44_HERSS
         (295 letters)



>FitnessBrowser__Putida:PP_1770
          Length = 746

 Score =  236 bits (602), Expect = 1e-66
 Identities = 125/281 (44%), Positives = 173/281 (61%)

Query: 4   KVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAVQGA 63
           ++V+ G+GLIGGSFA  LR +G    +VGV     S ++A  LG++D    D A+A  GA
Sbjct: 15  RLVVVGLGLIGGSFAKGLRESGLCREVVGVDLDAPSRKQAVALGVVDRCEEDLAAACVGA 74

Query: 64  DLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPAHPI 123
           D+I +A P+     +LA +A      AI+TD GS K +VV  AR   G R+ +F+P HPI
Sbjct: 75  DVIQLAVPILAMEKVLARLALLDLGDAIITDVGSAKGNVVREARAVFGARLPRFVPGHPI 134

Query: 124 AGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHDAVF 183
           AG E+ G EA+ A L+   KV++T L E D A + +V   WRA  A +  +S + HD V 
Sbjct: 135 AGSEQSGVEASNATLFRRHKVILTPLAETDPAALVLVDRLWRALDADVEHMSVERHDEVL 194

Query: 184 ASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANRDAL 243
           A+ SHLPH+LAF LVD +A +     +F+YAA GFRDFTRIA S P MW DI LANRDA+
Sbjct: 195 AATSHLPHLLAFGLVDSLAKRNENLEIFRYAAGGFRDFTRIAGSDPTMWHDIFLANRDAV 254

Query: 244 LTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284
           L  +D +   L  +R  IA GDG  +  ++  A+ AR+ ++
Sbjct: 255 LRTLDTFRSDLDALRDAIAEGDGHQLLGVFTRARVAREHFS 295


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: 538
Number of extensions: 22
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: 295
Length of database: 746
Length adjustment: 33
Effective length of query: 262
Effective length of database: 713
Effective search space:   186806
Effective search space used:   186806
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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