GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Cupriavidus basilensis 4G11

Align crotonase (EC 4.2.1.150) (characterized)
to candidate RR42_RS03015 RR42_RS03015 enoyl-CoA hydratase

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



>FitnessBrowser__Cup4G11:RR42_RS03015
          Length = 265

 Score =  167 bits (423), Expect = 2e-46
 Identities = 103/255 (40%), Positives = 150/255 (58%), Gaps = 7/255 (2%)

Query: 9   EKDGNVASITLNRPKALNALNAAT-LKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67
           E+ G++ ++T+N P+  N L   T + +   AI+ I  D +V AVIITG+G AF +G +I
Sbjct: 8   EQQGHIVTLTMNEPQRRNPLTGNTAVADFLEAIDRIHRDASVRAVIITGAGTAFSSGGNI 67

Query: 68  AEMK-----DLTAVEGRKFSVLG-NKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIR 121
            +M+      +  +E R+   LG  ++   L NLE PVIAA+NG A+G G +L+  CD+R
Sbjct: 68  RDMERQASGQVPGMEIRQDYRLGIQRLPLALFNLEVPVIAAVNGAAMGAGLDLACMCDMR 127

Query: 122 IASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKV 181
           IAS +A+F +  V LGI PG GG   L R IG+  A EL +TG+VI+A +AL   LV++V
Sbjct: 128 IASEQAQFAESFVKLGIIPGDGGAWLLPRVIGLARAAELTFTGQVIDARQALEWNLVSRV 187

Query: 182 VEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDR 241
           V PD+LL  A  L + I  N P AVR+ K  + + L   +DT +   A        T D 
Sbjct: 188 VPPDQLLPTANELAERIAANPPHAVRLAKRLLREALHTRLDTLLELSAGFQALSHQTSDH 247

Query: 242 VEGMTAFVEKRDKAF 256
            E ++AF++KR   F
Sbjct: 248 REAVSAFLDKRKPEF 262


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: 163
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: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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