GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Phaeobacter inhibens BS107

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate GFF1676 PGA1_c16990 putative enoyl-CoA hydratase FadB

Query= BRENDA::P77467
         (262 letters)



>FitnessBrowser__Phaeo:GFF1676
          Length = 258

 Score =  201 bits (512), Expect = 1e-56
 Identities = 106/258 (41%), Positives = 156/258 (60%), Gaps = 5/258 (1%)

Query: 5   ILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQ 64
           IL  +E G+  +TLNRP ++N+      A++   +++  ++   R ++LTG+G  FC+GQ
Sbjct: 6   ILFSLEDGLAVVTLNRPAKMNALTGLTRAEITHAMQRAGKE--ARAVVLTGSGVSFCSGQ 63

Query: 65  DLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIV 124
           DL+D     +    DL  ++   Y P++  +   P P I AVNG AAGAGA LAL  D+V
Sbjct: 64  DLSDA---ASQGKLDLERTLRDEYTPMLEAIYNCPVPTIAAVNGPAAGAGANLALAADVV 120

Query: 125 IAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQV 184
           IA  SA F+ AF+++GL+PD GGTW +PR  G A+AMG AL  +++SA+QA +WGMIW+ 
Sbjct: 121 IATESAYFMQAFARIGLMPDAGGTWFMPRQMGMAKAMGAALFADKISAKQASDWGMIWEA 180

Query: 185 VDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADY 244
           + D       +  A +LA+ PT   G IK AI     N+L  QL  E   Q   G++ D+
Sbjct: 181 IPDAEFDAHWRARAAYLASGPTRAFGAIKTAIRDGYGNSLPEQLSEEAHLQGQCGKTRDF 240

Query: 245 REGVSAFLAKRSPQFTGK 262
            EGV+AF+ KR  +F G+
Sbjct: 241 MEGVTAFMEKRPAKFEGR 258


Lambda     K      H
   0.321    0.136    0.403 

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: 156
Number of extensions: 9
Number of successful extensions: 3
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: 262
Length of database: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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: 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 (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