GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Cupriavidus basilensis 4G11

Align glutaminase (EC 3.5.1.2) (characterized)
to candidate RR42_RS27580 RR42_RS27580 glutaminase

Query= BRENDA::P0A6W0
         (308 letters)



>FitnessBrowser__Cup4G11:RR42_RS27580
          Length = 304

 Score =  283 bits (725), Expect = 3e-81
 Identities = 155/305 (50%), Positives = 199/305 (65%), Gaps = 2/305 (0%)

Query: 5   MDNA-ILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFS 63
           MD A IL+ I R + PL+ QG+VADYIP L  V  +  G+A+   DG+    GDA   FS
Sbjct: 1   MDYAHILQRIHRDIAPLLTQGRVADYIPELGKVPATHFGMALVFADGRSHCVGDAAVPFS 60

Query: 64  IQSISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVV 123
           IQSISK+ +  +A +   E+ +WQRVG++PSG+ FNSLVQLE EQG PRNPFINAGALVV
Sbjct: 61  IQSISKLFACTLAFQLLGED-LWQRVGREPSGNAFNSLVQLEYEQGKPRNPFINAGALVV 119

Query: 124 CDMLQGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHH 183
            D+L  R       M++ +R LSG   I YD  VA+SE EH+ RN A+A+ MK FG    
Sbjct: 120 TDVLCSRFVQAETAMVQFLRRLSGNPAIDYDPRVAQSEREHADRNRAMAYFMKDFGRLEM 179

Query: 184 DVTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGM 243
            V  V+  Y   CA+ MSC +LAR  +FLA+ G      E V+     ++++ALM T G 
Sbjct: 180 PVDKVIDAYCRQCAITMSCEDLARAALFLAHGGVVPWSGERVLDASPTKRLSALMLTCGT 239

Query: 244 YQNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQL 303
           Y  AG+F +RVGLPAKSGVGGGIVA++P   A+ VWSP LD +GNSLAG+  LE LT   
Sbjct: 240 YDAAGDFVYRVGLPAKSGVGGGIVAVLPGRWAVCVWSPGLDHSGNSLAGVQALEWLTTLS 299

Query: 304 GRSVY 308
           G S++
Sbjct: 300 GHSIF 304


Lambda     K      H
   0.321    0.135    0.395 

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: 272
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: 308
Length of database: 304
Length adjustment: 27
Effective length of query: 281
Effective length of database: 277
Effective search space:    77837
Effective search space used:    77837
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 (21.9 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