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_1164 N515DRAFT_1164 enoyl-CoA hydratase

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



>FitnessBrowser__Dyella79:N515DRAFT_1164
          Length = 260

 Score =  240 bits (612), Expect = 2e-68
 Identities = 126/260 (48%), Positives = 168/260 (64%), Gaps = 1/260 (0%)

Query: 1   MEFKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-K 59
           M ++N+ +   G V  IT+NRP  LNALN  TL E+  A    A+DD V  V++ G+G K
Sbjct: 1   MAYRNLDIGNRGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDK 60

Query: 60  AFVAGADIAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCD 119
           AFVAGADIAEM   T V+ + FS  G ++   +E L KPV+A I GFALGGG EL+++C 
Sbjct: 61  AFVAGADIAEMNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACH 120

Query: 120 IRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVN 179
           +R+AS KA+FGQPE+ LG+ PGFGGTQRL R  G G A EL  TG ++ A+ A  +G+VN
Sbjct: 121 LRVASEKARFGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVN 180

Query: 180 KVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATE 239
           +VV P+ L E   AL D +  +AP+A      AI QG +  +D G+ +E + F   F+TE
Sbjct: 181 RVVAPEALDETVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTE 240

Query: 240 DRVEGMTAFVEKRDKAFKNK 259
           D  EG TAF+EKR   FK +
Sbjct: 241 DMREGTTAFLEKRKAEFKGR 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: 182
Number of extensions: 9
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