GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citE in Cupriavidus basilensis 4G11

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 RR42_RS24350 RR42_RS24350 malyl-CoA thiolesterase

Query= SwissProt::P0A9I1
         (302 letters)



>FitnessBrowser__Cup4G11:RR42_RS24350
          Length = 292

 Score =  162 bits (410), Expect = 9e-45
 Identities = 89/282 (31%), Positives = 157/282 (55%), Gaps = 5/282 (1%)

Query: 10  KTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYR 69
           + R RRS+L+ PGAN   +  + +  AD  + DLED+VA   K+ AR  V  A++   Y 
Sbjct: 3   RNRHRRSVLYTPGANVRALEKAKLLNADGFILDLEDAVAPDAKEDARENVARAIESGGYG 62

Query: 70  DIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREP 129
             E +VR+N+LD++WG  DLE V R  AD + +PK ++A++V ++   ++ +       P
Sbjct: 63  GKEVLVRINSLDTKWGKGDLEIVARSAADGIVIPKVESAENVREVRAIMIEVGA-----P 117

Query: 130 GSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSI 189
            S  +   IE+P G+ RA EIA +  +L G+ +G  D  + L    +     +L +    
Sbjct: 118 ESMRIWCMIETPRGVLRAEEIAGSDAQLGGLIMGTSDLAKELGCAHTRMRLPMLASLGRC 177

Query: 190 LQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQK 249
           +  AR+ G+   D V+ D ++  GF       ++ GF+GK+LI+P+ ID  + +++P Q 
Sbjct: 178 VLVARAYGLSILDGVHLDLDDAKGFQLSCEQGREFGFNGKTLIHPKTIDKANEIFSPNQD 237

Query: 250 EVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVL 291
           E++ A++++ A      EG GVV ++G +++   +  A+ +L
Sbjct: 238 ELNWAKKIIAAYRQGVAEGKGVVVVDGHLIENLHVAAAQELL 279


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: 181
Number of extensions: 10
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: 292
Length adjustment: 26
Effective length of query: 276
Effective length of database: 266
Effective search space:    73416
Effective search space used:    73416
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 Sep 17 2021. 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