GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citE in Rhizobium etli CFN 42

Align Citrate lyase subunit beta; Citrase beta chain; Citrate (pro-3S)-lyase subunit beta; Citryl-CoA lyase subunit; EC 4.1.3.6; EC 4.1.3.34 (characterized)
to candidate WP_011427687.1 RHE_RS23145 CoA ester lyase

Query= SwissProt::P0A9I1
         (302 letters)



>NCBI__GCF_000092045.1:WP_011427687.1
          Length = 278

 Score =  102 bits (254), Expect = 1e-26
 Identities = 90/289 (31%), Positives = 133/289 (46%), Gaps = 25/289 (8%)

Query: 15  RSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDIET- 73
           RS+LFVPG      + +    ADA++ DLEDSVA   K  AR  V+  +Q    R  ET 
Sbjct: 4   RSLLFVPGDRPERFAKALASGADAVILDLEDSVAPPNKPKARDSVHEFVQR---RPGETK 60

Query: 74  -IVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGST 132
            ++R+N L S     DL A+       + LPK + A  VL +   +            +T
Sbjct: 61  LLIRINPLASPEFEGDLAALSGLQPFGLMLPKAEGAASVLKLASAL-----------AAT 109

Query: 133 GLLAAI--ESPLGITRAVEIAHASERLIGIALGAEDYVRNL--RTERSPEGT---ELLFA 185
            L+  I  E+P  I         S+ L G+  GAED    +   T R  +G        A
Sbjct: 110 ILILPIATETPSAIFEIGSYREVSDNLCGLTWGAEDLPAAIGATTARRTDGRYTPPYELA 169

Query: 186 RCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYA 245
           R   L AA +A + A DTVY D  +  G        ++ GF G   I+P Q++ +++ + 
Sbjct: 170 RSLTLFAAHAAAVPAIDTVYPDFRDLNGLRAYVGRARRDGFSGMMAIHPSQVETINHAFT 229

Query: 246 PTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRA 294
           P   E+  A +V   A  AA    GV+ L+G+M+D P +  A  +L+ A
Sbjct: 230 PDAFEIAWAEKV--TAAFAASPDAGVIQLDGRMLDLPHLKLAHRILASA 276


Lambda     K      H
   0.318    0.134    0.369 

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: 183
Number of extensions: 14
Number of successful extensions: 4
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: 302
Length of database: 278
Length adjustment: 26
Effective length of query: 276
Effective length of database: 252
Effective search space:    69552
Effective search space used:    69552
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: 48 (23.1 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