GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudarthrobacter sulfonivorans Ar51

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_058929110.1 AU252_RS00885 enoyl-CoA hydratase/isomerase family protein

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



>NCBI__GCF_001484605.1:WP_058929110.1
          Length = 258

 Score =  148 bits (374), Expect = 1e-40
 Identities = 86/247 (34%), Positives = 136/247 (55%), Gaps = 1/247 (0%)

Query: 11  DGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGADIAE 69
           D  +A+I +NRP+ +NA +A   K++      + +D  +   +ITG+G KAF AGAD+ +
Sbjct: 9   DDGIATIVMNRPERMNAFDAEAYKQLSEVWIRVRDDHAIRVAVITGAGEKAFSAGADLKD 68

Query: 70  MKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKF 129
           +          +    +++  +   + KPVIAA+NG+ LGGG  +  + DIRIA   A F
Sbjct: 69  LVPAPPELHDLWLTQKDQLLNRGLEIWKPVIAAVNGYCLGGGLTMLFATDIRIACHDATF 128

Query: 130 GQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLE 189
           G  EV  G+ PG G TQR+   +    A E++ TG+ I+A +AL  GL+N+VV+  +L+E
Sbjct: 129 GLSEVKRGVLPGNGATQRVIDNVSYPRAMEMLLTGEPIDASKALEWGLINEVVDRARLME 188

Query: 190 EAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAFV 249
            +  +   I  NAP+AV+  K    +    D+ +G+  E  +      +ED VEG  AF 
Sbjct: 189 RSLEIARQIAANAPLAVQATKELAVRSRSMDLASGLRLEQVLQRILQTSEDAVEGPKAFA 248

Query: 250 EKRDKAF 256
           E+R   F
Sbjct: 249 ERRPAVF 255


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: 150
Number of extensions: 10
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: 258
Length adjustment: 24
Effective length of query: 235
Effective length of database: 234
Effective search space:    54990
Effective search space used:    54990
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 Apr 09 2024. 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