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_055435184.1 ASC41_RS03100 pyridoxal-phosphate dependent enzyme

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



>NCBI__GCF_001418085.1:WP_055435184.1
          Length = 326

 Score =  215 bits (548), Expect = 1e-60
 Identities = 128/314 (40%), Positives = 183/314 (58%), Gaps = 19/314 (6%)

Query: 4   DNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHPG 63
           +NIL TIGNTPLV+IN L       + +K E FNP  SVKDR+AL+MIE AEA+G+L PG
Sbjct: 5   ENILGTIGNTPLVKINKLTAELPCLVLSKYETFNPGNSVKDRMALQMIEDAEADGRLKPG 64

Query: 64  STIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTDG 123
            TIIE TSGNTG+GLA+   +KGY  I VM++  S E+  ++KA GAE+++    +  + 
Sbjct: 65  GTIIEGTSGNTGMGLALAAIIKGYKCIFVMADKQSKEKVDILKAVGAEVVVCPTAVDPED 124

Query: 124 --AIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSG 181
             +   V++ + E     +  NQ+ N  N  AHY++T  EIW QT G +THFV  VGT G
Sbjct: 125 PRSYYSVSKRLGEETPNSWYVNQYDNPSNAKAHYQSTGPEIWEQTDGKITHFVVGVGTGG 184

Query: 182 TLMGVGKNLREKNPEIKI----IEAQPTKGHYIQGL-----------KSMEEAIVPAIYQ 226
           T+ GVGK L+E+NP IKI          K ++  G+           + + E I+P    
Sbjct: 185 TISGVGKYLKEQNPNIKIWGIDTYGSVFKKYHETGIFDEKEIYPYVTEGIGEDILPKNVD 244

Query: 227 ADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKI-DSGVIVVLFAD 285
            D ID    +  ++A    + +  +EG+F+G S+GAA+    +L E      V+VVLF D
Sbjct: 245 FDIIDGFTKVTDKDAAVYTQRLSKEEGMFLGNSAGAAIKGVLQLKEHFTKDDVVVVLFHD 304

Query: 286 RGEKYLSTKLFDTE 299
            G +Y+  K+F+ E
Sbjct: 305 HGSRYVG-KMFNDE 317


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: 343
Number of extensions: 22
Number of successful extensions: 4
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: 326
Length adjustment: 27
Effective length of query: 272
Effective length of database: 299
Effective search space:    81328
Effective search space used:    81328
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