GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PSSH in Lacinutrix algicola AKS293

Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_055435113.1 ASC41_RS02715 cysteine synthase CysM

Query= metacyc::MONOMER-20568
         (299 letters)



>NCBI__GCF_001418085.1:WP_055435113.1
          Length = 292

 Score =  266 bits (679), Expect = 5e-76
 Identities = 138/293 (47%), Positives = 192/293 (65%), Gaps = 2/293 (0%)

Query: 5   NILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPGS 64
           +IL+ IGNTPLV  ++L   P V++Y KLEG NP GSVKDR A  MI +A   G +  G 
Sbjct: 2   SILKQIGNTPLVEASNLVSKPNVKLYLKLEGNNPGGSVKDRPAYNMIAEAVKRGDIEKGG 61

Query: 65  TIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDGA 124
            I+EATSGNTGI LA +  + G  + +VM E  ++ER K ++A+GAE+ILT  + G +G+
Sbjct: 62  HIVEATSGNTGIALAYVASLFGIKISLVMPENSTVERIKTMRAYGAEVILTSAERGIEGS 121

Query: 125 IRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGTLM 184
            R VA  +++  G Y   NQF N+ N  AHYKTT  EIW  T G VTHFV+A+GT+GT+M
Sbjct: 122 -RDVAFKMRDEKG-YLLLNQFENDDNWKAHYKTTGPEIWRDTNGEVTHFVSAMGTTGTIM 179

Query: 185 GVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAFAK 244
           G    L+E+N  I+II AQP  G  I G++      VP+I+   K+D+ I +  E+A A 
Sbjct: 180 GTSTFLKEQNKNIQIIGAQPMDGSRIPGIRKWSPDYVPSIFNPSKVDQVIEVSQEQATAM 239

Query: 245 AREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLFD 297
            + +  +EG+F GMSSG ++  A KL E ID+G++V +  DRG++YLS+ LFD
Sbjct: 240 TKRLAREEGVFAGMSSGGSVATALKLIETIDTGIVVAIICDRGDRYLSSALFD 292


Lambda     K      H
   0.315    0.133    0.367 

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: 272
Number of extensions: 11
Number of successful extensions: 2
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: 299
Length of database: 292
Length adjustment: 26
Effective length of query: 273
Effective length of database: 266
Effective search space:    72618
Effective search space used:    72618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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