GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Ruegeria conchae TW15

Align 2-keto-4-pentenoate hydratase 3; EC 4.2.1.80; 2-hydroxypentadienoic acid hydratase 3 (uncharacterized)
to candidate WP_010441603.1 G7G_RS0111655 2-oxo-hepta-3-ene-1,7-dioic acid hydratase

Query= curated2:Q706S1
         (269 letters)



>NCBI__GCF_000192475.1:WP_010441603.1
          Length = 266

 Score =  174 bits (442), Expect = 1e-48
 Identities = 103/265 (38%), Positives = 143/265 (53%), Gaps = 6/265 (2%)

Query: 1   MTPQQREEAAQSLYQAMQSGKPIAPLRDTFPDMNVDDAYAIQSINTQRRISLGRRVVGRK 60
           MTP +  +AA  L  A +SG  I  L    P+M +DDAY +Q+   + +++ GR VVG K
Sbjct: 1   MTPAEHAKAAADLLDAERSGNQIGLLSLRHPEMGMDDAYEVQNAIYRAKLAEGRSVVGWK 60

Query: 61  IGLTSVVVQQQLGVDEPDFGALFDDMSFGDAETIPLSILHQPKVEAEIGFVLGRDLDTEQ 120
           IGLTS  +Q  L +D PD G LFDDM F +  T+P     QP++EAEI FV    L  + 
Sbjct: 61  IGLTSKAMQYALNIDIPDSGILFDDMIFDNGATVPADRFIQPRIEAEIAFVTKSPLGGDN 120

Query: 121 PTHQEVLQAVDYVVPALEIVGSRIADWNIK------FVDTVADNASSGVYVLGSTPISPR 174
            + ++V+ A DYV PA+EI+ +RI   + +        DT++DNA++   VLG+      
Sbjct: 121 VSREDVIAATDYVAPAIEILDTRIQRVDPETGKTRTVFDTISDNAANAGIVLGAARHKID 180

Query: 175 GLDLSLVGMCLSRRGEPVSTGAGAACLGTPLNAVVWLARTMSRLGKPLRAGELILSGALG 234
             DL  VG    R GE   TG GA  L  P+ +VVWLAR M+  G+ +  G++ILSG+  
Sbjct: 181 AADLRWVGALTFRNGEIEETGLGAGVLNDPIESVVWLARRMATYGQSIEPGQIILSGSFI 240

Query: 235 PMVAVKPGDVFECHINGVGSVRTEF 259
             V    G          GSV   F
Sbjct: 241 RPVECPSGTEIHADFGAFGSVDIRF 265


Lambda     K      H
   0.318    0.135    0.392 

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: 194
Number of extensions: 8
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: 269
Length of database: 266
Length adjustment: 25
Effective length of query: 244
Effective length of database: 241
Effective search space:    58804
Effective search space used:    58804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 24 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