GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcl in Rhizobium etli CFN 42

Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate WP_011427687.1 RHE_RS23145 CoA ester lyase

Query= BRENDA::Q9I562
         (275 letters)



>NCBI__GCF_000092045.1:WP_011427687.1
          Length = 278

 Score =  143 bits (361), Expect = 4e-39
 Identities = 108/278 (38%), Positives = 140/278 (50%), Gaps = 14/278 (5%)

Query: 6   VRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTP-EARVL 64
           +RS LFVP  RPER  KALASGAD VI+DLED+V    K +AR ++  F+   P E ++L
Sbjct: 3   LRSLLFVPGDRPERFAKALASGADAVILDLEDSVAPPNKPKARDSVHEFVQRRPGETKLL 62

Query: 65  VRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAAVASGKPVWPIVESARGLA 124
           +RIN    P    DLA         GL+LPK E AA V   A A    +  +  +    +
Sbjct: 63  IRINPLASPEFEGDLAALSG-LQPFGLMLPKAEGAASVLKLASALAATILILPIATETPS 121

Query: 125 ALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARY--------ALLLQTRLA 176
           A+ EI +   V     G    A DL    G+  A +  G  RY        +L L    A
Sbjct: 122 AIFEIGSYREVSDNLCGLTWGAEDLPAAIGATTARRTDG--RYTPPYELARSLTLFAAHA 179

Query: 177 GLAPPLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWAR 236
              P +D VYP  ++  GL   V  AR  GF G++ IHPSQVE I+    P   E+ WA 
Sbjct: 180 AAVPAIDTVYPDFRDLNGLRAYVGRARRDGFSGMMAIHPSQVETINHAFTPDAFEIAWAE 239

Query: 237 RVAEAGASG--AGVFVVDGEMVDAPVLGRARRLLERAG 272
           +V  A A+   AGV  +DG M+D P L  A R+L  AG
Sbjct: 240 KVTAAFAASPDAGVIQLDGRMLDLPHLKLAHRILASAG 277


Lambda     K      H
   0.320    0.137    0.394 

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: 174
Number of extensions: 11
Number of successful extensions: 5
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: 275
Length of database: 278
Length adjustment: 25
Effective length of query: 250
Effective length of database: 253
Effective search space:    63250
Effective search space used:    63250
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