GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Marinobacter adhaerens HP15

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate GFF1397 HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:D8IR44_HERSS
         (295 letters)



>lcl|FitnessBrowser__Marino:GFF1397 HP15_1364 3-phosphoshikimate
           1-carboxyvinyltransferase
          Length = 742

 Score =  243 bits (621), Expect = 7e-69
 Identities = 125/284 (44%), Positives = 173/284 (60%)

Query: 1   MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60
           +FK+V + G+GLIGGS A A+RR G A  +VG     + L+  +ELG+ID  A+  + AV
Sbjct: 7   LFKRVAVIGLGLIGGSLACAIRRKGLAVTVVGADHRTEELQLGKELGVIDQAASTVSDAV 66

Query: 61  QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120
           +GADL+++A PV  T  +L  I P LEP AI+TD GSTKS  VA      G      IP 
Sbjct: 67  RGADLVVLAVPVRATRAVLEQIRPALEPDAILTDVGSTKSSFVADVEAVFGGLSPLVIPG 126

Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180
           HPIAG EK G  AA  EL+   KV++T         +  +   W  CGA +  +S   HD
Sbjct: 127 HPIAGSEKSGIRAANPELFANHKVILTPPDNVSQPHLARLKGLWEGCGATVLTMSVAYHD 186

Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240
            V A+ SHLPH++AF+LVD +A +     +F+YAA GFRDFTRIAAS P MW DI L+NR
Sbjct: 187 EVLAATSHLPHLIAFSLVDTLAGEDENMDIFRYAAGGFRDFTRIAASDPVMWHDIFLSNR 246

Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284
           DA+L  +D +   L+ +R  IA  D   + ++++ A+ AR+ ++
Sbjct: 247 DAVLRVIDHFTHDLEQLRTAIANQDSATLLRVFSRAKAAREHFS 290


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: 502
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: 742
Length adjustment: 33
Effective length of query: 262
Effective length of database: 709
Effective search space:   185758
Effective search space used:   185758
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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