GapMind for Amino acid biosynthesis

 

Alignments for a candidate for Mt_cysM in Cupriavidus basilensis 4G11

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 RR42_RS21960 RR42_RS21960 cysteine synthase

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__Cup4G11:RR42_RS21960
          Length = 305

 Score =  199 bits (506), Expect = 7e-56
 Identities = 124/310 (40%), Positives = 171/310 (55%), Gaps = 19/310 (6%)

Query: 5   DSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEA 64
           D++LQ +GNTP + +QRL         G   ++W K E  NP GSIKDR A+ M+E AE 
Sbjct: 4   DNILQTIGNTPHIRVQRLF--------GDTHQVWIKSERANPGGSIKDRIALSMVEAAEQ 55

Query: 65  DGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSA 124
            G+L+PG TI+EPTSGNTGI LAM A +KGY+L+ VMP++ SVERR+L+  YGA    + 
Sbjct: 56  SGVLKPGGTIIEPTSGNTGIGLAMVAAVKGYKLVLVMPDSMSVERRRLMLAYGATFDLTP 115

Query: 125 AEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPE-ITHFVAGL 183
            E G   A+A A+EL A  P   M  Q+ NPAN ++H   T  E+LAD P+ I   V G+
Sbjct: 116 REKGMKGAIARAEELVAATPGAWMPQQFENPANIEAHVNTTALEILADFPQGIDALVTGV 175

Query: 184 GTTGTLMGTGRFLREHVANVKIVAAEPRYGEGV-------YALRNMDEGFVPELYDPEIL 236
           GT G + G  R L++    +K+ A EP     +       + ++ +  GF+P   D  +L
Sbjct: 176 GTGGHITGCARVLKQKWPALKVYAVEPVASPVISGGAPAPHPIQGIGAGFIPRNLDTALL 235

Query: 237 TARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADA 296
                V A  A    R     EG+  GIS+GA L AA+      L AG  A +     D 
Sbjct: 236 DGVIQVDAEPAREMARRAAREEGMLVGISSGATL-AAIAQKLPDLPAG--ATVLGFNYDT 292

Query: 297 GWKYLSTGAY 306
           G +YL+   +
Sbjct: 293 GERYLTVEGF 302


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: 293
Number of extensions: 16
Number of successful extensions: 3
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: 305
Length adjustment: 27
Effective length of query: 296
Effective length of database: 278
Effective search space:    82288
Effective search space used:    82288
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