GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Rhizobium etli CFN 42

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011424900.1 RHE_RS08035 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>NCBI__GCF_000092045.1:WP_011424900.1
          Length = 275

 Score =  120 bits (300), Expect = 4e-32
 Identities = 85/259 (32%), Positives = 129/259 (49%), Gaps = 10/259 (3%)

Query: 4   LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63
           L+ S +  VL L LN P A N L+ ALL  L+ ELE A  D  + V VI      F+AG 
Sbjct: 18  LLRSLRDGVLRLVLNDPPA-NVLSIALLEALMAELERAEADLDVRVVVIASTGLVFSAGH 76

Query: 64  DLNEMA----EKDLAATLNDTRPQLWARLQA----FNKPLIAAVNGYALGAGCELALLCD 115
           DL E+     ++D  A       +L A L        KP+IA V+G A  AGC+L   CD
Sbjct: 77  DLKELTAHRVDEDQGAAFFGKSFRLCADLMLKIAHVPKPVIAEVDGLATAAGCQLVASCD 136

Query: 116 VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVS 175
           + +  + + F  P + +G+         + R+  +  A +M+L+GE+I A  A+  GLV+
Sbjct: 137 LAICTDTSTFCTPGVNIGLFCSTPMVA-VSRAAHRKQAMEMLLTGETIDASTAKDFGLVN 195

Query: 176 DVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATE 235
            + P     +   + A+ +A  SPL L+  K+A  +  E+ ++A      ++      T 
Sbjct: 196 RIVPKQYLAQVVSKYAAVIAGKSPLTLKIGKEAFYRQLELPVEAAYDYASRVMVENMLTR 255

Query: 236 DRHEGISAFLQKRTPDFKG 254
           D  EGI AFL KR  ++KG
Sbjct: 256 DAQEGIGAFLGKRKSEWKG 274


Lambda     K      H
   0.318    0.130    0.356 

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: 114
Number of extensions: 9
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: 255
Length of database: 275
Length adjustment: 25
Effective length of query: 230
Effective length of database: 250
Effective search space:    57500
Effective search space used:    57500
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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