GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Erythrobacter marinus HWDM-33

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein

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



>NCBI__GCF_001013305.1:WP_047094365.1
          Length = 252

 Score =  114 bits (284), Expect = 3e-30
 Identities = 82/258 (31%), Positives = 130/258 (50%), Gaps = 15/258 (5%)

Query: 5   NIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGS--GKAFV 62
           N+ LE DG VA + ++R    NA N A  + +   +     D  V  ++I  +  G  F 
Sbjct: 2   NLRLEFDGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFC 61

Query: 63  AGADIAEM---KDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCD 119
           AGADI EM   KD  A      + + N++   L  L  P +A + G  +GGGC ++++CD
Sbjct: 62  AGADIKEMLLHKDDGAWLAANQAAI-NRVQHDLARLTLPTVAFVEGDCVGGGCGIAIACD 120

Query: 120 IRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVN 179
           +R+A+ KA+FG     LGI       + L   +G G AK +++TG +++A EA RIGLV 
Sbjct: 121 LRVATDKARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIGLV- 179

Query: 180 KVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEA-EVFGECFAT 238
                + + +  + L++ I+  +P ++R  K  + + L  D  TG   +   +F + F  
Sbjct: 180 -----EMIADSPRGLLNDILSASPHSIREIKMFVRRVL--DGQTGDDDQTLAIFTDAFMR 232

Query: 239 EDRVEGMTAFVEKRDKAF 256
            D  EG  AF  KR   F
Sbjct: 233 GDFAEGAAAFAGKRKPDF 250


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: 152
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: 252
Length adjustment: 24
Effective length of query: 235
Effective length of database: 228
Effective search space:    53580
Effective search space used:    53580
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