GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Echinicola vietnamensis KMM 6221, DSM 17526

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Echvi_0069 Echvi_0069 Enoyl-CoA hydratase/carnithine racemase

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



>FitnessBrowser__Cola:Echvi_0069
          Length = 260

 Score =  136 bits (342), Expect = 5e-37
 Identities = 84/260 (32%), Positives = 136/260 (52%), Gaps = 6/260 (2%)

Query: 1   MEFKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKA 60
           M++K I    + +   I ++RP   NALN   L+E+ AA +  A+ + V  V++TG G A
Sbjct: 1   MDYKYIRSSVNNHCQEIAIDRPAVFNALNFEVLEELKAAFDQAAQAETVRCVVLTGGGGA 60

Query: 61  FVAGADIAEMKDLTAVEGRKFSVLGNKIFRKL----ENLEKPVIAAINGFALGGGCELSL 116
           F +G D+  +   T ++G  F  +  K +  L     NL KP+I  +NG A+G GC L+L
Sbjct: 61  FCSGQDLKAVG--TDLDGIPFKEIIRKYYNPLIIQMRNLSKPIICKLNGAAVGAGCSLAL 118

Query: 117 SCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIG 176
           + D+ IAS +A   +    +G+    G    L + +G  +A EL  TG+ + AEEA R+G
Sbjct: 119 ATDVIIASKEAYLAEMFAHIGLVMDAGSNYFLPKRVGYPLAFELATTGRKVYAEEAERLG 178

Query: 177 LVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECF 236
           LVNK +E   L E     V+  +  +  A+ M K  + +     ++  +  EA    +  
Sbjct: 179 LVNKAIEHSALDETVAQYVEVYVNASGSAIGMIKEMLRKSNGMSLEEVLEMEAVYQEKAG 238

Query: 237 ATEDRVEGMTAFVEKRDKAF 256
           + +D  EG+T+F+EKR   F
Sbjct: 239 SHQDFKEGVTSFLEKRKPRF 258


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: 143
Number of extensions: 8
Number of successful extensions: 2
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: 260
Length adjustment: 24
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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