GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Cupriavidus basilensis 4G11

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate RR42_RS06465 RR42_RS06465 O-acetylhomoserine aminocarboxypropyltransferase

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__Cup4G11:RR42_RS06465
          Length = 436

 Score =  332 bits (852), Expect = 1e-95
 Identities = 180/434 (41%), Positives = 271/434 (62%), Gaps = 14/434 (3%)

Query: 3   SHFDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNP 62
           + FDT+ LHAG     D A  +RA PI+ TTS+VF++S+H + LF +E  G+VYSR  NP
Sbjct: 4   TRFDTLALHAGAAP--DPATGARATPIHLTTSFVFKDSEHAASLFNMERAGHVYSRISNP 61

Query: 63  TSNVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISF 122
           T  VLEERIAALE GA A+ V+SGQAA  LA+  L   G +IV++S LYGG++N    + 
Sbjct: 62  TVAVLEERIAALENGAGAIGVASGQAALHLAVATLMGAGSHIVASSALYGGSHNLLHYTL 121

Query: 123 KRFGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVV 182
           +RFGIE  FV+  + + +       TK ++ ET+GNP  +V D   +  +   +GIP++V
Sbjct: 122 RRFGIETTFVQARDIDAWRAAIRPETKLLFGETLGNPGLDVLDIPTLAQLGQDNGIPLLV 181

Query: 183 DNTFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQ 242
           D+TF    Y  +P   GA ++ HSATK++GGHGTTIGG++ + G F + +   +FP+ S+
Sbjct: 182 DSTF-TTPYLLKPFDLGAGLLYHSATKFLGGHGTTIGGVLAEGGTFDF-EASGRFPELSE 239

Query: 243 PAEGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGEN 302
           P  G+H  ++ E      +++  R E LRD G  ++P A++ LLQG+ETL LR  RH +N
Sbjct: 240 PYAGFHNMVFTEESTVAPFLLRARREGLRDFGACLSPMAAWQLLQGIETLPLRMARHVDN 299

Query: 303 ALKLAKWLEQSPYVSWVSYPGLASHSHHENAKKYLSNGFGGVLSFGVKDLPNADKETDPF 362
           A ++ ++L   P V  V+YP L SH  +  A++ L  G G V SF +K            
Sbjct: 300 ARRVVQFLVSHPMVESVAYPELESHPDYALARRLLPRGAGAVFSFNLKG----------N 349

Query: 363 KLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSVGIE 422
           + +G + +++L L S+LANVGDA++LVI P  TTH +++     A+G+++  IR+SVG+E
Sbjct: 350 RAAGQRFIESLALFSHLANVGDARSLVIHPASTTHFRMDAAALQAAGISEGTIRLSVGLE 409

Query: 423 FIDDIIADFQQSFE 436
             DD+I D ++  +
Sbjct: 410 DPDDLIDDLKRGLK 423


Lambda     K      H
   0.317    0.136    0.402 

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: 468
Number of extensions: 17
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: 444
Length of database: 436
Length adjustment: 32
Effective length of query: 412
Effective length of database: 404
Effective search space:   166448
Effective search space used:   166448
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: 51 (24.3 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