GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Shewanella loihica PV-4

Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate 5210267 Shew_2710 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)

Query= CharProtDB::CH_124469
         (429 letters)



>FitnessBrowser__PV4:5210267
          Length = 429

 Score =  437 bits (1124), Expect = e-127
 Identities = 225/426 (52%), Positives = 287/426 (67%), Gaps = 6/426 (1%)

Query: 9   ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68
           E+L LH G   +A T + AVPIY TTSY F D  HG  LF L+  G IY+R+MNPT DV 
Sbjct: 4   ESLALHHGYTSEATTKAAAVPIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTTDVL 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 EVRMAAFDDFDGLEAHIDDKTKALFCESIGNPAGNIVDIARLAEIAHRHGVPLIVDNTV- 182

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

Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308
           HG+V+T+ FG  A+   CR   LR+ G   +P   FLLLQGLETL+LRMERH  NA ALA
Sbjct: 243 HGVVYTQAFGPAAFIGRCRVVPLRNTGAALSPQSAFLLLQGLETLALRMERHCDNALALA 302

Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSRKV-----VNA 363
            +LE+ P+V+WV+Y  L++       +K        ++SFG K    ++ K      ++A
Sbjct: 303 NFLEQDPRVSWVNYGALDNSPYRDNCEKITSGKASGIISFGIKAEDSEAAKAAGGRFIDA 362

Query: 364 LKLASQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFA 423
           L++  +L N+GDAK+L   PA TTH QL  EE   AGV++DLIR++VGIEHI+DIIAD +
Sbjct: 363 LQMILRLVNIGDAKSLACHPATTTHRQLNGEELAKAGVSEDLIRISVGIEHIEDIIADVS 422

Query: 424 QALEVA 429
           QAL+ A
Sbjct: 423 QALDKA 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: 544
Number of extensions: 21
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: 429
Length of database: 429
Length adjustment: 32
Effective length of query: 397
Effective length of database: 397
Effective search space:   157609
Effective search space used:   157609
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:

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