GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Pseudomonas stutzeri RCH2

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate GFF1943 Psest_1986 3-phosphoshikimate 1-carboxyvinyltransferase

Query= uniprot:D8IR44_HERSS
         (295 letters)



>FitnessBrowser__psRCH2:GFF1943
          Length = 747

 Score =  223 bits (569), Expect = 8e-63
 Identities = 118/284 (41%), Positives = 165/284 (58%)

Query: 1   MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60
           +  ++V+ G+GLIGGSFA  LR AG    +VG     +S E A ELG++D  A   A A 
Sbjct: 13  ILNRLVVIGLGLIGGSFAKGLREAGLCREVVGFDLDARSRELAVELGVVDRCADTLAEAC 72

Query: 61  QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120
            GAD+I +A P+     +L  +A      A++TD GS K +VV  AR   G+   +F+P 
Sbjct: 73  HGADVIQLATPILALERLLGELAKLELGGAVITDVGSAKGNVVRCARNVFGEMPSRFVPG 132

Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180
           HPIAG E  G  AA + L+   KV++T L   D   + +V   W A GA +  +    HD
Sbjct: 133 HPIAGSELSGVTAANSTLFRRHKVILTPLENTDPQALALVTKLWSALGADVEHMGVAHHD 192

Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240
            V A+ SHLPH+LAF LVD +A +     +F+YAA GFRDFTRIA S P MW DI LANR
Sbjct: 193 EVLAATSHLPHLLAFGLVDSLAKRHENLEIFRYAAGGFRDFTRIAGSDPVMWHDIFLANR 252

Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284
           +A+L  +D +   L  +RA +  GDG  +  ++  A+ AR+ ++
Sbjct: 253 EAVLHTLDDFRADLDALRAAVDEGDGHRLLGVFTRAKAAREHFS 296


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: 519
Number of extensions: 24
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: 747
Length adjustment: 33
Effective length of query: 262
Effective length of database: 714
Effective search space:   187068
Effective search space used:   187068
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.

Links

Downloads

Related tools

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