GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Marinobacter adhaerens HP15

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate GFF4202 HP15_4142 naphthoate synthase

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



>FitnessBrowser__Marino:GFF4202
          Length = 260

 Score =  106 bits (265), Expect = 4e-28
 Identities = 83/259 (32%), Positives = 133/259 (51%), Gaps = 8/259 (3%)

Query: 1   MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59
           M +  IL+++ + VATIT+N P+  N        E+ +A      +  I ++VF  AG+K
Sbjct: 1   MTYEDILYDENNGVATITINRPDRYNAFRGQTCMELLDAFNRAGWNKDIGVIVFTGAGEK 60

Query: 60  AFCDGVDVADHVPEKVDE-MIDL-FHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDI 117
           AFC G D   H  +     +I L    + R +  +    +  VNG ++GGG  L   CD+
Sbjct: 61  AFCTGGDQGAHEGQYDGRGLIGLPVEELQRTIREVPKPVIARVNGFAIGGGHVLHVICDL 120

Query: 118 VIASEKAKIGQ--PEINLAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVN 175
            IASE A  GQ  P++  +V P    A+  +++G K+A E+    +  SA++A   GLVN
Sbjct: 121 SIASETAIFGQVGPKVG-SVDPGFGTAYLARVVGEKRAREIWYLCRKYSAQQALEWGLVN 179

Query: 176 VVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMAT 235
            V+P E   E  QK+  +   KS      A+R+  A  + D +  + A  +  +     T
Sbjct: 180 AVVPPEQLDEEVQKWCEEILEKSPTAISIAKRSFNA--DSDNIAGIGALGMQALSLYYDT 237

Query: 236 EDANEGLASFLEKRKPVFK 254
           +++ EG+ +FLEKRKP F+
Sbjct: 238 DESKEGVNAFLEKRKPEFR 256


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: 165
Number of extensions: 10
Number of successful extensions: 5
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: 260
Length adjustment: 24
Effective length of query: 232
Effective length of database: 236
Effective search space:    54752
Effective search space used:    54752
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