GapMind for Amino acid biosynthesis

 

Alignments for a candidate for Mt_cysM 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 SMc00421 SMc00421 O-acetylserine sulfhydrylase A

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__Smeli:SMc00421
          Length = 322

 Score =  200 bits (508), Expect = 4e-56
 Identities = 119/314 (37%), Positives = 173/314 (55%), Gaps = 16/314 (5%)

Query: 4   YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63
           + S+ + +G+TP+V L +L+        G    L AKLE  NP GS+KDR  V MIE  E
Sbjct: 13  FSSITETIGDTPIVRLDKLAKE-----KGVKANLLAKLEFFNPIGSVKDRIGVAMIESLE 67

Query: 64  ADGLLRPG-ATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122
           A G + PG  T++EPTSGNTGI+LA  A  KGYRLI  MPE  SVERR++L L GA+++ 
Sbjct: 68  AQGKITPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPETMSVERRKMLTLLGAELVL 127

Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181
           +    G   A+A A+EL  T P  ++  Q+ NPAN + H   T  E+  D    +   V+
Sbjct: 128 TEGAKGMKGAIAKAQELTETLPDAIIPQQFENPANPEIHRTTTAEEIWNDTEGAVDILVS 187

Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPE 234
           G+GT GT+ G G+ L+    +V+++A EP           G + ++ +  GF P + D  
Sbjct: 188 GIGTGGTITGAGQVLKARKPSVRVIAVEPEESPILSGGAPGPHKIQGIGAGFAPAILDTS 247

Query: 235 ILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVA 294
           +     +V A +A+   R +   EG+  GIS GA L AA+ VG     AG   +I +++ 
Sbjct: 248 VYDEVVTVNAGEAIEAARLVARLEGVPVGISAGAALQAAIEVGQREENAGR--NIVVIIP 305

Query: 295 DAGWKYLSTGAYAG 308
               +YLST  + G
Sbjct: 306 SFAERYLSTVLFEG 319


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: 258
Number of extensions: 14
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: 323
Length of database: 322
Length adjustment: 28
Effective length of query: 295
Effective length of database: 294
Effective search space:    86730
Effective search space used:    86730
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