GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N2C3

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate AO356_23665 AO356_23665 hypothetical protein

Query= BRENDA::P37887
         (308 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23665
          Length = 318

 Score = 66.2 bits (160), Expect = 9e-16
 Identities = 56/165 (33%), Positives = 79/165 (47%), Gaps = 14/165 (8%)

Query: 23  LADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLKAGNTIIEPTSGNTGIGLAM 82
           LA+     V++K E   P  + K R GL  +   ++E     G  I+  T GN G  LA+
Sbjct: 31  LAERLGCTVWVKHENHTPTGAFKVRGGLTFVHWLKREHPEAKG--IVTATRGNHGQSLAL 88

Query: 83  VAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGMKGAIKKAEELAEKHG-YFV 141
            A A GLKA++V+P   S+E+ N +R +G E+V          A ++A  LA   G Y V
Sbjct: 89  AATALGLKALIVVPQGNSVEKNNAMRGFGGEVV--EYGRDFDEAREEAARLAHAQGLYLV 146

Query: 142 PQQFNNPSNPEIHR--QTTGKEIVEQFGDDQLDAFVAGIGTGGTI 184
           P     P +PE+ R   T G E+ +   D  LD     IG G  I
Sbjct: 147 P-----PFHPELVRGVATYGLELFKAVPD--LDTVYVPIGCGSGI 184


Lambda     K      H
   0.313    0.134    0.373 

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: 182
Number of extensions: 5
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: 308
Length of database: 318
Length adjustment: 27
Effective length of query: 281
Effective length of database: 291
Effective search space:    81771
Effective search space used:    81771
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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