GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Cupriavidus basilensis 4G11

Align Lmo2664 protein (characterized, see rationale)
to candidate RR42_RS09405 RR42_RS09405 butanediol dehydrogenase

Query= uniprot:Q8Y413
         (350 letters)



>FitnessBrowser__Cup4G11:RR42_RS09405
          Length = 357

 Score =  171 bits (433), Expect = 3e-47
 Identities = 116/362 (32%), Positives = 184/362 (50%), Gaps = 28/362 (7%)

Query: 1   MRAAVLYENNVIKAEQI---DEATCGKDQVRVEVKAVGICGSDIHK-------MQTRWKY 50
           M+AAV    + ++ E++   D+   G   V++ V   GICGSD+H+       +     +
Sbjct: 1   MKAAVWRGRHDVRVEEVRVPDKPAEG--WVKIRVHWCGICGSDLHEYVAGPVFIPVDHPH 58

Query: 51  PLPA-----VMGHEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNY 105
           PL       ++GHEF+G I E+G+ VT   +G+RV     + C +C YC  G + +C++ 
Sbjct: 59  PLTGLKGQCILGHEFSGEIAELGAGVTGFKVGERVTADACQHCGKCYYCTHGLYNICESL 118

Query: 106 RMVGSHFHGGFAENVVMKADNVISIGD-LDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIV 164
              G   +G FAE V + A+ +  + +    E GA+IEPLAV +H V      +G TV+V
Sbjct: 119 AFTGLMNNGAFAEYVNVPAELLYKLPENFPTEAGALIEPLAVGLHAVKKAGNIVGQTVVV 178

Query: 165 FGIGTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTN 224
            G GTIG+  + C   AG   IIA+++S  +   A E G    I+PK  D   +V A T 
Sbjct: 179 VGAGTIGLCTIMCAKAAGAGRIIALEMSSARKKKALEVGANVVIDPKECDAIAQVKALTG 238

Query: 225 GLGADIALECAGSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGF 284
           G GAD++ EC G+K T +  + V +K GK   +GI        E +  N F    T K  
Sbjct: 239 GYGADVSFECIGNKATAKLAIDVIRKAGKCVMVGI------FEEPSAFNFFEIVSTEKEI 292

Query: 285 WNSYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEE-TKEAFDMILSREHDYNKVMI 343
             S +      E+   I F+  GRI ++PLI+ R  L +   + F+ +++ +    K+++
Sbjct: 293 IGSLAY---NGEFADVIRFIADGRIDVQPLITGRISLADIVSQGFEELVNNKDGNVKIIV 349

Query: 344 LP 345
            P
Sbjct: 350 QP 351


Lambda     K      H
   0.321    0.139    0.417 

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: 343
Number of extensions: 18
Number of successful extensions: 4
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: 350
Length of database: 357
Length adjustment: 29
Effective length of query: 321
Effective length of database: 328
Effective search space:   105288
Effective search space used:   105288
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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