GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Marinobacter adhaerens HP15

Align O-acetylhomoserine sulfhydrylase protein; EC 2.3.1.31 (characterized, see rationale)
to candidate GFF659 HP15_641 homocysteine synthase

Query= uniprot:D8J1Y3_HERSS
         (413 letters)



>FitnessBrowser__Marino:GFF659
          Length = 425

 Score =  236 bits (603), Expect = 7e-67
 Identities = 145/417 (34%), Positives = 229/417 (54%), Gaps = 15/417 (3%)

Query: 11  TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70
           T  LH+  +      +   PI+ + ++ ++D +  A++F  K  G  Y R  NPT A LE
Sbjct: 5   TLALHAGFKSDPTTRAATTPIYQTTSYTFDDTQHGADLFDLKVQGNIYTRIMNPTNAVLE 64

Query: 71  DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129
           +++ ++E G   +  A+GMAAI   +Q + + G+++VS++ L+G T +L+  ++  QG +
Sbjct: 65  ERMAELEGGVGALAVASGMAAITYALQTICKVGNNIVSTSQLYGGTYNLFAHSLPNQGIE 124

Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189
             MV   D   VE AI  NTR +F E+I NP   V D++R  E+  + GI  +VDNT+ +
Sbjct: 125 CKMVRHDDFDAVEKAIDENTRALFCESIGNPAGNVVDIQRWAEIAHKHGIPLMVDNTVAT 184

Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDW----TRYPHIAEN------ 239
           P+L RP   GA +V++SLTK IGGHG  + G + D+G+FDW     ++P + E       
Sbjct: 185 PFLCRPIEHGADIVIHSLTKYIGGHGTTVAGVVVDSGKFDWKASADKFPMLNEPDPSYHG 244

Query: 240 --YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297
             Y     P   + + R   LR+ G +L P  A  I  G ET+ALR ER C+NA  +A  
Sbjct: 245 VVYTDALGPAAFIGRCRVVPLRNTGAALAPFNAFLIMQGLETLALRMERHCENAEKVANF 304

Query: 298 LQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGIDC-FDYLNRLRLAIPT 355
           LQ    V  V Y  L + P  A  + +     S ++SF +K G +    +++ L L +  
Sbjct: 305 LQEHPSVEWVNYATLANSPYKATCEKISGGKASGILSFGIKGGREAGAKFIDALELILRL 364

Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412
            N+GD ++L    A T   ++  E   S G++E L+R+S+G+E  DD++AD  QALD
Sbjct: 365 VNIGDAKSLACHPATTTHRQLNPEELKSAGVSEDLVRLSIGIEHVDDIIADITQALD 421


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: 449
Number of extensions: 26
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: 413
Length of database: 425
Length adjustment: 32
Effective length of query: 381
Effective length of database: 393
Effective search space:   149733
Effective search space used:   149733
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: 50 (23.9 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