GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metY in Shewanella sp. ANA-3

Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate 7023700 Shewana3_0930 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)

Query= CharProtDB::CH_124469
         (429 letters)



>lcl|FitnessBrowser__ANA3:7023700 Shewana3_0930
           O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
          Length = 430

 Score =  440 bits (1131), Expect = e-128
 Identities = 231/426 (54%), Positives = 288/426 (67%), Gaps = 6/426 (1%)

Query: 9   ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68
           E+L LH G E +A T + AVPIY TTSY F D  HG  LF L+  G IY+R+MNPT+ V 
Sbjct: 4   ESLALHHGYESEATTKAAAVPIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTSSVL 63

Query: 69  EKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLGI 128
           E+R+AA+E G  A+A +SG +A+  A+  L + GDNIVSTS LYGGTYNLF  TLPR G+
Sbjct: 64  EQRLAAIEGGIGALALASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQGV 123

Query: 129 TTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTFG 188
             +    DD  +L A ID  TKA++ ESIGNP  N+ D +R+AE+AH  GVPL+VDNT  
Sbjct: 124 EVRMAAFDDFEELDALIDAKTKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIVDNTV- 182

Query: 189 GGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPGY 248
               L RP +HGADIV HS TK+IGGHGTTIGGVI+DSGKFDW  N +RF   N+  P Y
Sbjct: 183 ATPVLCRPFEHGADIVIHSLTKYIGGHGTTIGGVIIDSGKFDWVANKERFALLNQADPSY 242

Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308
           HG+V+TE FG  A+   CR   LR+ G   +P   FLLLQGLETLSLRMERH  NA ALA
Sbjct: 243 HGVVYTEAFGAAAFIGRCRVVPLRNTGAALSPHSAFLLLQGLETLSLRMERHCSNALALA 302

Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGG-PDQSR----KVVNA 363
           +YL  HP V+WV+Y  L S    +  +K        ++SFG K   P++ +    K ++A
Sbjct: 303 EYLILHPSVSWVNYGALPSSPYRENCQKITGGKASGIISFGIKAATPEEGKIAGGKFIDA 362

Query: 364 LKLASQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFA 423
           L++  +L N+GDAK+L   PA TTH QL   E   AGV++DLIR++VGIEHIDDIIAD A
Sbjct: 363 LQMILRLVNIGDAKSLACHPASTTHRQLDANELARAGVSEDLIRISVGIEHIDDIIADVA 422

Query: 424 QALEVA 429
           QALE A
Sbjct: 423 QALEKA 428


Lambda     K      H
   0.318    0.135    0.399 

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: 532
Number of extensions: 19
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: 429
Length of database: 430
Length adjustment: 32
Effective length of query: 397
Effective length of database: 398
Effective search space:   158006
Effective search space used:   158006
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 (21.7 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 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