GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Dyella japonica UNC79MFTsu3.2

Align crotonase (EC 4.2.1.150) (characterized)
to candidate N515DRAFT_0930 N515DRAFT_0930 methylglutaconyl-CoA hydratase

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0930
          Length = 264

 Score =  125 bits (315), Expect = 7e-34
 Identities = 85/263 (32%), Positives = 137/263 (52%), Gaps = 13/263 (4%)

Query: 3   FKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFV 62
           + ++ L     V ++T+NRP+  NA + + + E+  A+     D+NV AV++TG+G +F 
Sbjct: 2   YTSLQLADRAGVRTVTMNRPQVHNAFDDSLIAELTDALAAAGRDENVRAVVLTGAGASFS 61

Query: 63  AGADIAEMKDL---TAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCD 119
           AGAD+  M+ +   +  E R+ S+    + R L+ L KP +A +NG A GGG  L   CD
Sbjct: 62  AGADLNWMRGMAKASEAENREDSLRLAALMRTLQFLPKPTVARVNGAAYGGGVGLIACCD 121

Query: 120 IRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVN 179
           I I    AKFG  EV LG+ P       +A AIG+  ++ L  TG++ +A  A RIGL++
Sbjct: 122 IAIGVDSAKFGLTEVKLGLVPAVISPYVIA-AIGLRQSRRLFLTGELFDASTAQRIGLLH 180

Query: 180 KVVEPDKLLEEAKALVDAIIVNAPIAVRMCK------AAINQGLQCDIDTGVAYEAEVFG 233
           + V  ++L +    ++ A     P+A    K      A  +Q     ID      AE+  
Sbjct: 181 QCVRAEELDDALAGVLAAFAKAGPVAQAQAKRLALRVAGQDQAQAERID---RENAELIA 237

Query: 234 ECFATEDRVEGMTAFVEKRDKAF 256
               + +  EG+ AF++KR  A+
Sbjct: 238 RLRVSAEGQEGLGAFLDKRAAAW 260


Lambda     K      H
   0.318    0.136    0.376 

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: 148
Number of extensions: 11
Number of successful extensions: 3
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: 259
Length of database: 264
Length adjustment: 25
Effective length of query: 234
Effective length of database: 239
Effective search space:    55926
Effective search space used:    55926
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 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