GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Pseudomonas fluorescens FW300-N2E3

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate AO353_02060 AO353_02060 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:D8IR44_HERSS
         (295 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_02060
          Length = 735

 Score =  233 bits (593), Expect = 1e-65
 Identities = 123/284 (43%), Positives = 173/284 (60%)

Query: 1   MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60
           M  ++V+ G+GLIGGSFA  LR +G    +VGV    QS + A ELG++D    D A+A 
Sbjct: 1   MIGRLVVIGLGLIGGSFAKGLRESGLCREVVGVDLDPQSRKLAVELGVVDRCEDDLATAC 60

Query: 61  QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120
            GAD+I +A P+     +L  +A      AI+TD GS K +VV AA  A G    +F+P 
Sbjct: 61  CGADVIQLAVPILAMEKLLVLLAGMDLGAAILTDVGSAKGNVVRAATEAFGGMPARFVPG 120

Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180
           HPIAG E+ G EA+ A+L+   KV++T L + D A + +V   WR  GA +  +  + HD
Sbjct: 121 HPIAGSEQSGVEASNAQLFRRHKVILTPLEQTDPAALAVVDRLWRELGADVEHMQVERHD 180

Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240
            V A+ SHLPH+LAF LVD +A +     +F+YAA GFRDFTRIA S P MW DI LANR
Sbjct: 181 EVLAATSHLPHLLAFGLVDSLAKRSENLEIFRYAAGGFRDFTRIAGSDPVMWHDIFLANR 240

Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284
           +A+L  +D +   L  +R  + AGDG  +  ++  A+ AR+ ++
Sbjct: 241 EAVLRTLDTFRSDLDALRDAVDAGDGHQLLGVFTRARVAREHFS 284


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: 500
Number of extensions: 15
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: 735
Length adjustment: 33
Effective length of query: 262
Effective length of database: 702
Effective search space:   183924
Effective search space used:   183924
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 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