GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HDOP-hydrol in Pseudomonas fluorescens FW300-N1B4

Align FAA hydrolase family protein (characterized, see rationale)
to candidate Pf1N1B4_2275 Fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2275 Fumarylacetoacetate
           hydrolase family protein
          Length = 221

 Score =  107 bits (266), Expect = 3e-28
 Identities = 64/183 (34%), Positives = 99/183 (54%), Gaps = 5/183 (2%)

Query: 70  IGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGV 129
           +GK +CIG NYA+HA E + P+P EP++F K  S VV       IP       +E E+ V
Sbjct: 17  LGKVVCIGRNYAEHAKELDNPVPTEPLLFIKPGSCVVPLEGGFSIPTERGSVHYEAEIAV 76

Query: 130 VIGKG-GSYIDEKDAMSHVAGYCVVNDVSEREYQIE---RGGTWDKGKGCDTFGPIGPWL 185
           +IGK   +    ++ +  ++G     D++ R+ Q E   +G  W+  K  D    I P+ 
Sbjct: 77  LIGKPLSTKPSREEVLDAISGIAPALDLTLRDKQAELKAKGLPWEIAKSFDGAAVIAPF- 135

Query: 186 VTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPP 245
           V     AD   +G+ L ++G+  Q+GN+  M+  +  ++ Y++   SLQ GDVI TGTP 
Sbjct: 136 VAGSTFADLTDIGIRLTINGEVRQDGNSKDMLNPIVPMIQYMAGCFSLQAGDVILTGTPV 195

Query: 246 GVG 248
           GVG
Sbjct: 196 GVG 198


Lambda     K      H
   0.316    0.138    0.419 

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: 190
Number of extensions: 10
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: 281
Length of database: 221
Length adjustment: 24
Effective length of query: 257
Effective length of database: 197
Effective search space:    50629
Effective search space used:    50629
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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