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_011427269.1 RHE_RS20895 CoA ester lyase

Query= SwissProt::P0A9I1
         (302 letters)



>NCBI__GCF_000092045.1:WP_011427269.1
          Length = 301

 Score =  139 bits (351), Expect = 6e-38
 Identities = 93/297 (31%), Positives = 148/297 (49%), Gaps = 9/297 (3%)

Query: 9   RKTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLY 68
           R +  RRS+L VP  N   +  S     DA++FDLEDSVA  +K+ AR  +      P  
Sbjct: 8   RSSSLRRSVLSVPAINLRALEKSRSLDCDAVIFDLEDSVAPEKKEEARENLRRFFAGPPL 67

Query: 69  RDIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGRE 128
              E I+R+N+L SE+G  DL+ V     D V LPK D  QDV D+      + +A  +E
Sbjct: 68  EGKERIIRINSLSSEFGPADLDLVKEVSPDAVLLPKVDEPQDVTDVGD---LLTEADAQE 124

Query: 129 PGSTGLLAAIESPLGITRAVEIAH----ASERLIGIALGAEDYVRNLRTERSPEGTELLF 184
                + A IE+P G+     IA        RL  + +G  D  +       P  T L+ 
Sbjct: 125 --EVRIWAMIETPRGVLNVGAIAEFGHTPGSRLDCLVVGLNDLRKETGVLPQPGRTYLVP 182

Query: 185 ARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLY 244
               ++ A ++ G+ A D+V++D  +  GF  E    + +GF GK LI+P QI   +  +
Sbjct: 183 WLMQVILAVKAYGLDALDSVFNDFRDGEGFEAECGQGRAMGFAGKMLIHPTQIAAANRHF 242

Query: 245 APTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAELSGIRE 301
            P+ +E+  A+ ++ A    A  GL V++ NG+M++   + +A  ++ +A L   R+
Sbjct: 243 GPSAEEIAEAQAIISAFADPAARGLNVINANGRMIERLHLVQAEALVHKARLISARK 299


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: 189
Number of extensions: 7
Number of successful extensions: 2
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: 301
Length adjustment: 27
Effective length of query: 275
Effective length of database: 274
Effective search space:    75350
Effective search space used:    75350
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