GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Marinobacter adhaerens HP15

Align 2-oxopent-4-enoate hydratase subunit (EC 4.2.1.80) (characterized)
to candidate GFF1138 HP15_1116 hydratase/decarboxylase

Query= metacyc::MONOMER-3403
         (222 letters)



>FitnessBrowser__Marino:GFF1138
          Length = 264

 Score =  162 bits (409), Expect = 7e-45
 Identities = 93/224 (41%), Positives = 128/224 (57%), Gaps = 5/224 (2%)

Query: 1   MDKTLINE----LGDELYQAMVQRETVTPLTSRGFDISVEDAYHISLRMLERRLAAGERV 56
           M KTL  E    L + +  A +Q   +T +T+   D++ EDAY +   +  R+ A G ++
Sbjct: 1   MSKTLSQEQVLALAEHVENAELQAHDITKVTNDFPDMTFEDAYDVQWEIRRRKEARGNKI 60

Query: 57  IGKKIGVTSKAVQNMLGVHQPDFGYLTDAMVYNSGEAMPISEKLIQPRAEGEIAFILKKD 116
           +G K+G+TS A    +GV  P +G+L D      G  +   E LI P+ E EIAF+ K  
Sbjct: 61  VGMKMGLTSWAKMAQMGVETPIYGFLADYFSVPDGGVVNTKE-LIHPKIEAEIAFVTKAP 119

Query: 117 LMGPGVTNADVLAATECVIPCFEVVDSRIQDWKIKIQDTVADNASCGLFVLGDQAVSPRQ 176
           L GPG     VLAAT+ VIP  EV+DSR +++K  +   VADNAS   F+ G Q      
Sbjct: 120 LKGPGCHIGQVLAATDFVIPAVEVIDSRYENFKFDLVSVVADNASSTRFITGGQMADVAD 179

Query: 177 VDLVTCGMLVEKNGQLLSTGAGAAALGSPVNCVAWLANTLGHFG 220
           VDL T G++VEKNG+++  GAGAA LG P + VA LAN L   G
Sbjct: 180 VDLKTLGVVVEKNGEVVDVGAGAAVLGHPASSVAMLANLLAERG 223


Lambda     K      H
   0.319    0.136    0.395 

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: 117
Number of extensions: 2
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: 222
Length of database: 264
Length adjustment: 23
Effective length of query: 199
Effective length of database: 241
Effective search space:    47959
Effective search space used:    47959
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: 46 (22.3 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