GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PSSH in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_4297 N515DRAFT_4297 cystathionine beta-synthase (EC 4.2.1.22)

Query= BRENDA::P9WP53
         (323 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4297
          Length = 456

 Score =  176 bits (445), Expect = 1e-48
 Identities = 112/320 (35%), Positives = 168/320 (52%), Gaps = 29/320 (9%)

Query: 1   MTRYDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIE 60
           MT + S+L+ +G TP+V  QRL        D     L+ KLE  NP GSIKDR  + MIE
Sbjct: 1   MTVHQSVLELIGRTPMVRAQRL--------DAGSCELFLKLESANPGGSIKDRIGLSMIE 52

Query: 61  QAEADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQI 120
            AE  G ++PGAT++E T+GNTG+ LA+ A+ KGYRL+ V+P+  S E+   L+  GA++
Sbjct: 53  GAERAGKIKPGATLVEGTAGNTGLGLALVAQQKGYRLVLVVPDKMSREKIFNLKAMGAEV 112

Query: 121 IFS---AAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EI 176
           + +    A+G        A+ +A   P    + Q+GNP N  +H   TGPE+L  +   +
Sbjct: 113 VLTRSDVAKGHPEYYQDMAERIARETPGAYFINQFGNPDNPAAHIATTGPEILEQMDGRV 172

Query: 177 THFVAGLGTTGTLMGTGRFLREHVANVKIVAAEP-------RYGEGV-------YALRNM 222
              V G G++GT+ G  R+  EH  + +IV A+P          EGV       + +  +
Sbjct: 173 DAIVVGCGSSGTMSGLSRYFAEHSPDTEIVLADPVGSILAQYINEGVLSTKSGSWMVEGI 232

Query: 223 DEGFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALA 282
            E F+P + D   +   Y++   ++    REL+  EG+  G STG +L AAL        
Sbjct: 233 GEDFLPSISDFSRVRKAYAISDKESFLAARELLAKEGVLGGSSTGTLLSAALKY---CRE 289

Query: 283 AGERADIALVVADAGWKYLS 302
             +   +  +V D G KYLS
Sbjct: 290 QTQPKRVVTLVCDTGNKYLS 309


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: 360
Number of extensions: 17
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: 456
Length adjustment: 30
Effective length of query: 293
Effective length of database: 426
Effective search space:   124818
Effective search space used:   124818
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: 50 (23.9 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