GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuE in Cupriavidus basilensis 4G11

Align 3-hydroxy-3-methylglutaryl-CoA lyase, cytoplasmic; 3-hydroxy-3-methylglutaryl-CoA lyase-like protein 1; EC 4.1.3.4 (characterized)
to candidate RR42_RS12425 RR42_RS12425 3-hydroxy-3-methylglutaryl-CoA lyase

Query= SwissProt::D4A5C3
         (343 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS12425 RR42_RS12425
           3-hydroxy-3-methylglutaryl-CoA lyase
          Length = 326

 Score =  188 bits (478), Expect = 1e-52
 Identities = 112/319 (35%), Positives = 170/319 (53%), Gaps = 16/319 (5%)

Query: 39  SQLSGLPEYVKIVEVGPRDGLQNEKVIVPTDIKIEFINQLSQTGLSVIEVTSFVSSRWVP 98
           + +   P    I EVG RDGLQ+   I+PT  K E+I      G   IEV SFV ++ +P
Sbjct: 3   THIPSAPRQAVIREVGLRDGLQSIATILPTSAKREWIQAAYAAGQREIEVGSFVPAKLLP 62

Query: 99  QMADHAEVMGGIHQYPGVRYPVLVPNLQGLQHAVAAGATEIAVFGAASESFSKKNINCSI 158
           Q+AD AE++      PG+   VLVPNL+G Q+A+A+GA  + V  +AS + S  N+  + 
Sbjct: 63  QLADTAELVDFARSLPGLFVSVLVPNLRGAQNAIASGADLMLVPLSASHAHSLANLRKTP 122

Query: 159 EESMGRFEQVISS--ARHMNIPVRGYVSCALGCPYEGSIMPQKVTEVSKRLYSMGCYEIS 216
           +E +    ++ +   A      + G V  A GC  +G + P++V  + + L   G   +S
Sbjct: 123 DEVVAEVARIRAERDAAGSRTLIEGGVGTAFGCTIQGHVDPEEVLRLMQALLDAGADRVS 182

Query: 217 LGDTVGVGTPGSMKTMLESVMKEIPPGALAVHCHDTYGQALANILTALQMGINVVDSAVS 276
           L DTVG   PG ++ + E             H HDT G  LAN+  AL+ G+   D+ ++
Sbjct: 183 LADTVGYADPGMVRRLFERATALAGDRFWCGHFHDTRGLGLANVHAALEAGVTRFDACLA 242

Query: 277 GLGGCPYAKGASGNVATEDLIYMLNGMGLNTGVDLHKVMEAGDFIC-------------- 322
           G+GGCP+A GASGNVATEDL Y+L  MG +TG+D+ +++   + +               
Sbjct: 243 GIGGCPHAPGASGNVATEDLAYLLGSMGFDTGIDIGRLLALRERVAGWLTNETLHGTLWR 302

Query: 323 KAVNKTTNSKVAQASFKAR 341
             + KT  + VA A+F+ R
Sbjct: 303 AGLPKTFPASVADAAFRLR 321


Lambda     K      H
   0.316    0.132    0.385 

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: 301
Number of extensions: 9
Number of successful extensions: 3
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: 343
Length of database: 326
Length adjustment: 28
Effective length of query: 315
Effective length of database: 298
Effective search space:    93870
Effective search space used:    93870
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 (21.6 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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