GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS12425
          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:

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