Aligments for a candidate for cysK in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis