GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Limnohabitans curvus MWH-C5

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase

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



>NCBI__GCF_003063475.1:WP_108402835.1
          Length = 268

 Score =  173 bits (439), Expect = 3e-48
 Identities = 102/251 (40%), Positives = 141/251 (56%), Gaps = 6/251 (2%)

Query: 13  NVASITLNRPKALNALNA---ATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGADIA 68
           +V  + LNRP+  NALN      L ++   + D+  D  +  V++TG+G K F  G D+ 
Sbjct: 20  HVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGD--LRCVVLTGAGAKIFCGGGDLK 77

Query: 69  EMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAK 128
           E   +T    +    +  +++  L +L  PVI AING A GGG E++L CD   AS  A+
Sbjct: 78  ERNGMTPQAWQYQHEIFERLYWALIDLPLPVIGAINGHAYGGGLEMALCCDFLYASQDAR 137

Query: 129 FGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLL 188
           F  PEV LGI PG GGTQ L RA+G   AKEL  TG+  +AE+AL  GLVN+V  PD +L
Sbjct: 138 FALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAWGLVNQVAAPDAVL 197

Query: 189 EEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAF 248
             A      I  NAP++VR  K +I  G Q ++ T   +E E +     T+DR EG+ AF
Sbjct: 198 ALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRLVDTDDRREGVAAF 257

Query: 249 VEKRDKAFKNK 259
            +KR   FK +
Sbjct: 258 NDKRPPVFKGR 268


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: 156
Number of extensions: 7
Number of successful extensions: 1
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: 268
Length adjustment: 25
Effective length of query: 234
Effective length of database: 243
Effective search space:    56862
Effective search space used:    56862
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