GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Rhizobium etli CFN 42

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011425014.1 RHE_RS08795 enoyl-CoA hydratase/isomerase family protein

Query= metacyc::MONOMER-15953
         (257 letters)



>NCBI__GCF_000092045.1:WP_011425014.1
          Length = 259

 Score =  147 bits (370), Expect = 3e-40
 Identities = 98/257 (38%), Positives = 132/257 (51%), Gaps = 8/257 (3%)

Query: 4   TLSVDAPEQGVRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAA 63
           T+ VD  ++ V ++T+ RPE LNAL+  +L  LA      E + + R  VLTG  K F+A
Sbjct: 5   TVRVDV-DRHVAILTISRPEKLNALDLDMLKALADAADAVEANPDLRVAVLTGEGKGFSA 63

Query: 64  GADIKEMAERDLVGILEDPRVAH----WQRIAAFSKPLIAAVNGFCLGGGCELAMHADIL 119
           G DIK      L  +     V H    ++R+A    PLIAA+NG  LGGG ELA  ADI 
Sbjct: 64  GGDIKAWGGM-LPQVFGHAWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAGVADIR 122

Query: 120 IAGEDARFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEV 179
           +A E  + G PE  LG++PG  GTQRL+R  G     +M L G+   A  A+  G+V  V
Sbjct: 123 VAEEHIKIGLPETGLGMVPGWSGTQRLVRRFGAQAVRRMALGGEIFTAEEARLLGIVDAV 182

Query: 180 TLPELTIERALAIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADR 239
                ++  A   A  IA + P AV +AK  +  A   D  +G   E     + A T D 
Sbjct: 183 VPTGNSVAAARQYAGRIAARGPAAVEIAKLMIASANGED--NGTAVEALGSILAAKTGDL 240

Query: 240 AEGIRAFQEKRRPEFTG 256
            EG+ +F EKR   F G
Sbjct: 241 KEGVASFSEKRPATFKG 257


Lambda     K      H
   0.320    0.134    0.374 

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: 207
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: 257
Length of database: 259
Length adjustment: 24
Effective length of query: 233
Effective length of database: 235
Effective search space:    54755
Effective search space used:    54755
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 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