GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Cupriavidus basilensis 4G11

Align O-acetylhomoserine sulfhydrylase protein; EC 2.3.1.31 (characterized, see rationale)
to candidate RR42_RS06465 RR42_RS06465 O-acetylhomoserine aminocarboxypropyltransferase

Query= uniprot:D8J1Y3_HERSS
         (413 letters)



>FitnessBrowser__Cup4G11:RR42_RS06465
          Length = 436

 Score =  263 bits (673), Expect = 6e-75
 Identities = 159/421 (37%), Positives = 234/421 (55%), Gaps = 18/421 (4%)

Query: 9   FTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAA 68
           F T  LH+        G+   PIH + +F ++D+   A +F  ++ G+ Y R  NPTVA 
Sbjct: 6   FDTLALHAGAAPDPATGARATPIHLTTSFVFKDSEHAASLFNMERAGHVYSRISNPTVAV 65

Query: 69  LEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSLWMTVGAQG 127
           LE++I  +E+G   I  A+G AA+   V  L+  G H+V+S+ L+G + N L  T+   G
Sbjct: 66  LEERIAALENGAGAIGVASGQAALHLAVATLMGAGSHIVASSALYGGSHNLLHYTLRRFG 125

Query: 128 AKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTM 187
            + + V A D+    AAI   T+L+F ET+ NP   V D+  + +L ++ GI  +VD+T 
Sbjct: 126 IETTFVQARDIDAWRAAIRPETKLLFGETLGNPGLDVLDIPTLAQLGQDNGIPLLVDSTF 185

Query: 188 TSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHIAENY---- 240
           T+PYL +P  +GAGL+ +S TK +GGHG  +GG L + G FD+    R+P ++E Y    
Sbjct: 186 TTPYLLKPFDLGAGLLYHSATKFLGGHGTTIGGVLAEGGTFDFEASGRFPELSEPYAGFH 245

Query: 241 ------KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALAL 294
                 +   AP   + + R + LRDFG  L P AA  +  G ET+ LR  R   NA  +
Sbjct: 246 NMVFTEESTVAP--FLLRARREGLRDFGACLSPMAAWQLLQGIETLPLRMARHVDNARRV 303

Query: 295 AQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDCFD-YLNRLRLA 352
            Q L +   V +V YP LESHP +AL++ L  R  G++ SF LK        ++  L L 
Sbjct: 304 VQFLVSHPMVESVAYPELESHPDYALARRLLPRGAGAVFSFNLKGNRAAGQRFIESLALF 363

Query: 353 IPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412
              +N+GD R+LVI  A T  + M A    + GI+E  IR+SVGLED DDL+ D ++ L 
Sbjct: 364 SHLANVGDARSLVIHPASTTHFRMDAAALQAAGISEGTIRLSVGLEDPDDLIDDLKRGLK 423

Query: 413 A 413
           A
Sbjct: 424 A 424


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: 431
Number of extensions: 22
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: 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 (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