GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PSSH in Sinorhizobium meliloti 1021

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 SMc01174 SMc01174 cysteine synthase A

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__Smeli:SMc01174
          Length = 361

 Score =  132 bits (333), Expect = 1e-35
 Identities = 102/318 (32%), Positives = 152/318 (47%), Gaps = 31/318 (9%)

Query: 6   SLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEAD 65
           S+L+A+GNTPL+ L+ +S       +     +  K E  NP  S+KDR A+ +I QAE  
Sbjct: 21  SVLEAIGNTPLIRLKAVS-------EATGCNILGKAEFLNPGQSVKDRAALWIIRQAEKS 73

Query: 66  GLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAA 125
           G LRPG  I+E T+GNTGI LA+     GYR + V+PE  S E++  L L GA+++   A
Sbjct: 74  GQLRPGGVIVEGTAGNTGIGLAVVGSALGYRTVIVIPETQSQEKKDALRLLGAELVEVPA 133

Query: 126 EGGSN------TAVATAKELAATNPSW-VMLYQYGNPANTDSHYCGTGPELLADLP-EIT 177
               N       +   A +LA T P+  +   Q+ N AN  +H   T PE+  D   ++ 
Sbjct: 134 VPYRNPNNYVKISGRLAAQLAETEPNGAIWANQFDNVANRQAHVDTTAPEIWRDTDGKVD 193

Query: 178 HFVAGLGTTGTLMGTGRFLREHVANVKIVAAEPR---------YGE----GVYALRNMDE 224
            F+  +G+ GTL G    LR   A +KI  A+P          +GE    G      + +
Sbjct: 194 GFICAVGSGGTLAGVAEGLRARNAAIKIGIADPEGAALYNFYAHGELKSSGSSITEGIGQ 253

Query: 225 GFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAG 284
           G +    +       Y +   +AV    +L+  EGI  G STG  +  A+ +   A   G
Sbjct: 254 GRITANLEDFTPDFAYQIPDAEAVPYVFDLIEKEGICVGGSTGINIAGAVRL---ARDLG 310

Query: 285 ERADIALVVADAGWKYLS 302
               I  ++ D G +Y S
Sbjct: 311 PGHTIVTILCDYGNRYQS 328


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: 310
Number of extensions: 13
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: 361
Length adjustment: 29
Effective length of query: 294
Effective length of database: 332
Effective search space:    97608
Effective search space used:    97608
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: 49 (23.5 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