GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Phaeobacter inhibens BS107

Align BadI (characterized)
to candidate GFF2642 PGA1_c26820 probable enoyl-CoA hydratase PaaG

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__Phaeo:GFF2642
          Length = 261

 Score = 97.8 bits (242), Expect = 2e-25
 Identities = 81/264 (30%), Positives = 118/264 (44%), Gaps = 18/264 (6%)

Query: 4   EDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFC 63
           E L+ E       I +NRPD++N+F        ++A  +A  D    A++L GAG R FC
Sbjct: 3   ETLLVEDHGTWVEITLNRPDRLNSFT-EEMHHALRAALEAARDGGARAVLLTGAG-RGFC 60

Query: 64  TGGDQSTHD-----GNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATIC 118
            G D    D     G  D   TV      L   IR +  PVI  V G A G G  LA  C
Sbjct: 61  AGQDLGDRDPRKMDGPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALAC 120

Query: 119 DLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178
           D+ + +E A F Q   K+G +    G+  L R++GE +A+ +    +    K+AE  GL 
Sbjct: 121 DVVLAAESAKFIQSFSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGLI 180

Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMG------MYALK 232
              VP +EL AE +   E+        L + K+     T   A +  +         A+K
Sbjct: 181 WKAVPDEELMAEARAMAEKFANGPTLGLGLTKQ-----TIQAAAVTTLSDQLEIEADAMK 235

Query: 233 LYYDTDESREGVKALQEKRKPEFR 256
              ++ +  EGV +  EKR P F+
Sbjct: 236 TCGESADYAEGVASFLEKRVPAFK 259


Lambda     K      H
   0.319    0.138    0.418 

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: 175
Number of extensions: 15
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 (21.7 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 (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