GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metZ in Echinicola vietnamensis KMM 6221, DSM 17526

Align O-acetylhomoserine sulfhydrylase protein; EC 2.3.1.31 (characterized, see rationale)
to candidate Echvi_3411 Echvi_3411 OAH/OAS sulfhydrylase

Query= uniprot:D8J1Y3_HERSS
         (413 letters)



>lcl|FitnessBrowser__Cola:Echvi_3411 Echvi_3411 OAH/OAS
           sulfhydrylase
          Length = 436

 Score =  225 bits (574), Expect = 2e-63
 Identities = 142/426 (33%), Positives = 228/426 (53%), Gaps = 22/426 (5%)

Query: 7   YGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTV 66
           + F T  LH+  +      S   PI+ + ++ +  A   A +F  K+ G  Y R  NPT 
Sbjct: 6   FKFETLQLHAGHEPDSNTNSRAVPIYQTSSYVFNSAEHGANLFGLKEFGNIYTRIMNPTN 65

Query: 67  AALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGA 125
              E ++  +E G + +  ++G AA    +  +L  GD+ V+S FL+G T N   ++   
Sbjct: 66  DVFEKRMAALEGGVAALAVSSGQAAQFIALSNILENGDNFVTSPFLYGGTYNQFKVSFKR 125

Query: 126 QGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDN 185
            G       +   +++E  I   T+ ++VETI NP   V D + +  L ++  I  VVDN
Sbjct: 126 LGISARFASSEKAEDMEKLIDDRTKALYVETIGNPGFNVPDFEALSALSKKHDIPLVVDN 185

Query: 186 TM-TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAE---- 238
           T     YLFRP   GA +VV S TK IGGHG ++GG + D G ++W   ++P  +E    
Sbjct: 186 TFGAGGYLFRPLAHGAHIVVASATKWIGGHGTSIGGIIVDGGNYNWGNGKFPQFSEPSEG 245

Query: 239 ----NY-----KKNPAPQWGMA---QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQER 286
               N+     + NP     +A   + R + LRDFG ++ P  +  +  G ET++LR ER
Sbjct: 246 YHGLNFWEVFGEGNPLGLPNIAFSIRARVEGLRDFGPAISPFNSFLLLQGLETLSLRAER 305

Query: 287 ECKNALALAQMLQADERVAAVYYPGLESHPQHALSKA-LFRSFGSLMSFELKDGIDCFDY 345
             +NAL LA+ L+   +VA V YPGLESH  H L+K  L + FG +++FE+K G +  + 
Sbjct: 306 TVENALTLAKWLENHPQVATVSYPGLESHGHHTLAKKYLKKGFGGVLTFEVKGGKEAGEK 365

Query: 346 L-NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLV 404
           L + L+L    +N+GD +TL+I  + T   ++  + +A+ G+   ++R+S+G+E  DD+ 
Sbjct: 366 LVDSLQLISHLANVGDAKTLIIQPSATTHQQLSEKEQAAAGVTPGMLRISLGIEHIDDIC 425

Query: 405 ADFRQA 410
           AD  QA
Sbjct: 426 ADLEQA 431


Lambda     K      H
   0.319    0.134    0.391 

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: 462
Number of extensions: 21
Number of successful extensions: 6
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: 413
Length of database: 436
Length adjustment: 32
Effective length of query: 381
Effective length of database: 404
Effective search space:   153924
Effective search space used:   153924
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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