GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citE in Nocardiopsis lucentensis DSM 44048

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_017598633.1 D471_RS0110795 CoA ester lyase

Query= SwissProt::P0A9I1
         (302 letters)



>NCBI__GCF_000341125.1:WP_017598633.1
          Length = 315

 Score =  155 bits (391), Expect = 1e-42
 Identities = 106/302 (35%), Positives = 154/302 (50%), Gaps = 13/302 (4%)

Query: 12  RTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDI 71
           R+RRS+L VPG+N   V  +     DA   DLED+VA  EK  AR  V  AL    +   
Sbjct: 5   RSRRSVLAVPGSNPRFVEKARGLDVDAFFLDLEDAVAPLEKAAARENVVRALNDGGWDGK 64

Query: 72  ETIVRVNALDSEWGVNDLEAVVRGGA---DVVRLPKTDTAQDVLDIEKEILRIEKACGRE 128
              VRVN + +EW   D+  VV G     D + LPK  + +DV  ++  + +IE+A G E
Sbjct: 65  LRSVRVNDVSTEWAYRDVITVVEGAGAELDCLVLPKVTSPRDVHWLDTLLTQIERAVGLE 124

Query: 129 PGSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRT------ERSP---EG 179
            G  G+ A IE   G+T    IA AS RL  +  G  D++ +L        E+ P    G
Sbjct: 125 VGRIGIEAQIEDARGLTEVDAIAAASPRLESLVYGPADFMASLNMKSLVVGEQPPGYDTG 184

Query: 180 TELLFARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDL 239
               +    IL AAR+ G+QA D  Y    +   F + AA    LGFDGK +++P Q++ 
Sbjct: 185 DAYHYVLMRILTAARAHGLQAVDGPYLQIRDVDAFRRSAARTAALGFDGKWVLHPLQVEA 244

Query: 240 LHNLYAPTQKEVDHARRVVEA-AEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAELSG 298
            + +YAPTQ++ DHA  +++A A A   +  G V L  +M+D      A +V  +   +G
Sbjct: 245 ANEVYAPTQEDYDHAELILDAYAHATTVDRRGAVMLGDEMLDEASRKMALVVAGKGRAAG 304

Query: 299 IR 300
           +R
Sbjct: 305 LR 306


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: 224
Number of extensions: 15
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: 302
Length of database: 315
Length adjustment: 27
Effective length of query: 275
Effective length of database: 288
Effective search space:    79200
Effective search space used:    79200
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