GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas fluorescens GW456-L13

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate PfGW456L13_2434 Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2434
          Length = 257

 Score =  110 bits (274), Expect = 4e-29
 Identities = 76/243 (31%), Positives = 118/243 (48%), Gaps = 5/243 (2%)

Query: 14  VATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVADHVP 72
           V  ITL  P + N LT  ++ E+   L   + DP  + +V      KAF  G D+ +   
Sbjct: 14  VRLITLQRPQALNALTTELLGELAAELNIAQADPDTRAVVLT-GSRKAFAAGADIKEMAE 72

Query: 73  -EKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVIASEKAKIGQPEI 131
            + V  + D     ++ +       +  VNG +LGGGCEL    DI+IA E A+ GQPEI
Sbjct: 73  RDLVGILDDPRQASWQAITRFSKPLIAAVNGFALGGGCELAMHADIIIAGEDARFGQPEI 132

Query: 132 NLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVEGFREAAQKF 190
           NL + P         + +G   AM+++LTG+ I A++A+ +GLV+ V   E   E A   
Sbjct: 133 NLGIMPGAGGTQRLLRAVGKSMAMQMVLTGESIDARQAQRVGLVSEVTQPEFTVERALHI 192

Query: 191 MADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDANEGLASFLEKRK 250
                +K+      A+ A++  ++ D    L+     +      T D +EG+A+F EKR 
Sbjct: 193 AHSIAAKAPLAVRLAKEALLKAMDTDLATGLRFERHAFTV-LAGTRDRDEGIAAFQEKRS 251

Query: 251 PVF 253
           P F
Sbjct: 252 PTF 254


Lambda     K      H
   0.322    0.136    0.401 

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: 136
Number of extensions: 8
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: 256
Length of database: 257
Length adjustment: 24
Effective length of query: 232
Effective length of database: 233
Effective search space:    54056
Effective search space used:    54056
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 (21.9 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