GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Novosphingobium fuchskuhlense FNE08-7

Align Enoyl-CoA-hydratase; EC 4.2.1.17 (characterized)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase

Query= SwissProt::G4V4T7
         (265 letters)



>NCBI__GCF_001519075.1:WP_156424864.1
          Length = 277

 Score =  198 bits (504), Expect = 9e-56
 Identities = 117/267 (43%), Positives = 154/267 (57%), Gaps = 12/267 (4%)

Query: 2   SETRVRYEKKDHVAYVTMDRPAVLNAMDRRMHEELAGIWDDVEADDDVRAVVLTGAGDRA 61
           S   +  E++  V  +T+ RPAVLNA++ RMHEEL   ++   ADD     V+TG G R 
Sbjct: 20  SMEHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQG-RG 78

Query: 62  FSVGQDLKERARLNESGVAPTTFGSGGQAGHPRLTDRFTLSKPVVARVRGYALGGGFELV 121
           F  G DLK         VA   F S    G+  L +RF   KP++A V G ALGGGFE+ 
Sbjct: 79  FCAGSDLK--------AVAAEGFRSYPAHGYAGLIERFDCDKPIIAAVNGLALGGGFEVA 130

Query: 122 LACDIVIAAEDAVFALPEVRLGLIAGAGGVFRLPRQLPQKVAMGYLLTGRRMDAATALRH 181
           LACD++IAAE A F LPE R+G +A  GG+ RL RQ+  K AMG +L+ R +DAA   R 
Sbjct: 131 LACDLIIAAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERL 190

Query: 182 GLVNEVVPAAELDQCVADWTDSLVRAAPLSVRAIKEAALRSVD---LPLEEAFTTSYHWE 238
           G V EVVP  +L+  V  W ++++  APLS+RA K+A +R +D   +    A    Y   
Sbjct: 191 GFVTEVVPDTDLESAVERWVEAILLGAPLSIRASKQAVMRGLDEAGVAAAMAAQPGYPAF 250

Query: 239 ERRRRSADAIEGVRAFAEKRDPIWTGQ 265
                SAD  EG  AFAEKR P+W G+
Sbjct: 251 AAWSASADLREGTTAFAEKRPPVWQGR 277


Lambda     K      H
   0.320    0.136    0.399 

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: 221
Number of extensions: 14
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: 265
Length of database: 277
Length adjustment: 25
Effective length of query: 240
Effective length of database: 252
Effective search space:    60480
Effective search space used:    60480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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