GapMind for catabolism of small carbon sources

 

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

Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MEB0
         (258 letters)



>NCBI__GCF_001519075.1:WP_156424864.1
          Length = 277

 Score =  150 bits (379), Expect = 3e-41
 Identities = 99/266 (37%), Positives = 143/266 (53%), Gaps = 21/266 (7%)

Query: 4   ENILVETRGRVGLVTLSRPKALNALNDALMDELGVALREFDADDAIGAIVLTGSEKAFAA 63
           E+I VE RGRV  +TL+RP  LNA+N  + +EL  A   F ADD     V+TG  + F A
Sbjct: 22  EHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQGRGFCA 81

Query: 64  GADIGMMSTYSYMDVYKGDY--ITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDMIF 121
           G+D+  ++   +       Y  +   ++      KPIIAAV G ALGGG E+A+ CD+I 
Sbjct: 82  GSDLKAVAAEGFRSYPAHGYAGLIERFDC----DKPIIAAVNGLALGGGFEVALACDLII 137

Query: 122 AADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVI 181
           AA++A+FG PE ++G +   GG  RL R +   +AM + L+AR +DAAE ER G V+ V+
Sbjct: 138 AAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERLGFVTEVV 197

Query: 182 PAASLID------ESIAAGATIAEFPLPAVMMVKESVNRAYE---TTLAEGVHFERRLFH 232
           P   L        E+I  GA +      ++   K++V R  +      A         F 
Sbjct: 198 PDTDLESAVERWVEAILLGAPL------SIRASKQAVMRGLDEAGVAAAMAAQPGYPAFA 251

Query: 233 SLFATEDQKEGMAAFVEKRKPVFKHR 258
           +  A+ D +EG  AF EKR PV++ R
Sbjct: 252 AWSASADLREGTTAFAEKRPPVWQGR 277


Lambda     K      H
   0.322    0.135    0.383 

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: 205
Number of extensions: 12
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: 258
Length of database: 277
Length adjustment: 25
Effective length of query: 233
Effective length of database: 252
Effective search space:    58716
Effective search space used:    58716
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 (21.9 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