GapMind for Amino acid biosynthesis

 

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

Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate AO356_04305 AO356_04305 cysteine synthase

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_04305
          Length = 324

 Score =  172 bits (437), Expect = 8e-48
 Identities = 111/322 (34%), Positives = 171/322 (53%), Gaps = 26/322 (8%)

Query: 10  ALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLR 69
           ++GNTPLV + R++PR         V + AK+E RNP  S+K R    MI  AE+ G L+
Sbjct: 11  SIGNTPLVQINRIAPRG--------VTILAKIEGRNPGYSVKCRIGANMIWDAESSGKLK 62

Query: 70  PGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGS 129
           PG TI+EPTSGNTGI LA  A  +GY+L+  MP + S+ERR++L+  GA+++ +    G 
Sbjct: 63  PGMTIVEPTSGNTGIGLAFVAAARGYKLMLTMPASMSIERRKVLKALGAELVLTEPAKGM 122

Query: 130 NTAVATAKELAATNPS-WVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGTTG 187
             A+  A E+ A++PS + M  Q+ NPAN   H   TGPE+  D    +   VAG+GT G
Sbjct: 123 KGAIEKAAEILASDPSKYFMPQQFDNPANPAIHEKTTGPEIWNDTDGAVDVLVAGVGTGG 182

Query: 188 TLMGTGRFLREHVAN-VKIVAAEPRYGEGV-------------YALRNMDEGFVPELYDP 233
           T+ G  R+++      +  VA EP     +             + ++ +  GFVP+  D 
Sbjct: 183 TITGVSRYIKNTCGKPILSVAVEPEVSPVITQAMAGHEIKPSPHKIQGIGAGFVPKNLDL 242

Query: 234 EILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVV 293
            I+     V   ++      L+  EGI  GIS GA +  A+ +       G+   I +++
Sbjct: 243 SIVDLVERVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEMQGK--TIVVIL 300

Query: 294 ADAGWKYLSTGAYAGSLDDAET 315
            D+G +YLS+  ++    + ET
Sbjct: 301 PDSGERYLSSMLFSDLFTEQET 322


Lambda     K      H
   0.317    0.134    0.398 

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: 294
Number of extensions: 22
Number of successful extensions: 5
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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: 41 (21.6 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