GapMind for catabolism of small carbon sources

 

Alignments for a candidate for KDF-hydrolase in Herbaspirillum seropedicae SmR1

Align 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway) protein; EC 4.2.1.80 (characterized, see rationale)
to candidate HSERO_RS17860 HSERO_RS17860 5-carboxymethyl-2-hydroxymuconate isomerase

Query= uniprot:D8INW0
         (281 letters)



>FitnessBrowser__HerbieS:HSERO_RS17860
          Length = 227

 Score =  115 bits (287), Expect = 1e-30
 Identities = 75/213 (35%), Positives = 108/213 (50%), Gaps = 13/213 (6%)

Query: 63  IGACVGNIGKFICIGLNYADHAAE-SNLPIPAEPVVFNKWTSAVVGPNDNVKIPRGSKKT 121
           +G     + +  C+G NYA HA E  + P    P  F K   AVV  +  V  P  +   
Sbjct: 16  VGGAAFPVRRIYCVGRNYAAHAREMGHDPDREPPFFFMKPADAVVPTDSVVPYPVATSDY 75

Query: 122 DWEVELGVIIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIER---GGTWDKGKGCDTF 178
             E+EL V + KGG  I  + A+  V GY V  D++ R+ Q +    G  WD  KG D  
Sbjct: 76  HHEIELVVALAKGGRNIPVEQALELVFGYAVGLDMTRRDIQSQAKKLGRPWDMAKGFDQS 135

Query: 179 GPIGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFNVAHIVSYLSRFMSLQPGDV 238
            P  P +V   +   P +  +WL+V+G+  Q G+ + +I++VA  +SYLS  + L PGD+
Sbjct: 136 APCAP-IVPVAQAGHPDQGAVWLKVNGEVRQQGDLADLIWSVAETISYLSGLVELFPGDL 194

Query: 239 ISTGTPPGVGMGVKPEAVYLRAGQTIRLGIDGL 271
           I TGTP GVG  VK        G  ++  +DGL
Sbjct: 195 IFTGTPEGVGAVVK--------GDKLQGHVDGL 219


Lambda     K      H
   0.316    0.139    0.421 

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: 182
Number of extensions: 9
Number of successful extensions: 4
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: 227
Length adjustment: 24
Effective length of query: 257
Effective length of database: 203
Effective search space:    52171
Effective search space used:    52171
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 (21.6 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 (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