GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaG in Herbaspirillum seropedicae SmR1

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase

Query= BRENDA::Q5SLK3
         (254 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19405 HSERO_RS19405 enoyl-CoA
           hydratase
          Length = 258

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/250 (35%), Positives = 138/250 (55%), Gaps = 4/250 (1%)

Query: 5   ERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDLT 64
           E  + V ++ L+RP+ LNA++  L+  L  AL   +   E+  +++TG+ +AF+AG D++
Sbjct: 9   ETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGSEKAFAAGADIS 68

Query: 65  EFGDRKPDYEAHLRR--YNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVGA 122
                  DY    +     R  E L  + KP++ AV G A G G  LA+  D  +AA  A
Sbjct: 69  AMAGY--DYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMMCDFIIAADNA 126

Query: 123 SFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEKL 182
            F    +++G+VP +G +  LPR V  AKA +L L    + AEEA   GLV R+V A+KL
Sbjct: 127 KFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLVSRIVAADKL 186

Query: 183 MEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVRA 242
           +EEA++ A  +A+ P +   + K  +   Y  +L+E +  E  L      T+D +EG++A
Sbjct: 187 LEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALFYSCFATEDQKEGMKA 246

Query: 243 FREKRPPRFQ 252
           F EKR P F+
Sbjct: 247 FLEKRQPVFK 256


Lambda     K      H
   0.318    0.135    0.371 

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: 163
Number of extensions: 9
Number of successful extensions: 2
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: 254
Length of database: 258
Length adjustment: 24
Effective length of query: 230
Effective length of database: 234
Effective search space:    53820
Effective search space used:    53820
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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.

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