GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Pseudomonas fluorescens FW300-N2C3

Align glutaminase (EC 3.5.1.2) (characterized)
to candidate AO356_21690 AO356_21690 glutaminase A

Query= BRENDA::P0A6W0
         (308 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21690
          Length = 302

 Score =  364 bits (935), Expect = e-105
 Identities = 183/301 (60%), Positives = 232/301 (77%), Gaps = 1/301 (0%)

Query: 8   AILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSI 67
           A+L  IL  VRPLIGQGKVADYIPAL TV  ++LGIA+   DG+L+ AGDA+  FS+QSI
Sbjct: 3   ALLNEILDAVRPLIGQGKVADYIPALGTVVPNQLGIAVYGNDGELYCAGDAETAFSVQSI 62

Query: 68  SKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCDML 127
           SKV SLV A+ H S E IW+R+G +PSG PFNSLVQLE E+G PRNPFINAGALV+CD+ 
Sbjct: 63  SKVFSLVQAIGH-SGEAIWERLGHEPSGQPFNSLVQLEFERGRPRNPFINAGALVICDIN 121

Query: 128 QGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDVTT 187
           Q R +AP   M + VR LSG   +  D  VA SE++H ARNAA+A+LM+SFGNFH+DV  
Sbjct: 122 QSRFAAPALSMRDFVRRLSGNPQVMVDGKVAESEYQHRARNAAMAYLMQSFGNFHNDVEA 181

Query: 188 VLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQNA 247
           VL++YF +CAL+MSC++LAR F FLAN G   H  E +++  Q +Q+N++MATSG+Y  A
Sbjct: 182 VLRSYFSHCALRMSCIDLARAFCFLANDGFCKHSGEQILSARQTQQVNSIMATSGLYDEA 241

Query: 248 GEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGRSV 307
           G FA+RVGLP KSGVGGGIVA+VP    + VWSPEL+ AGNSLAG+A LE +++++G SV
Sbjct: 242 GNFAYRVGLPGKSGVGGGIVAVVPGRFTVCVWSPELNAAGNSLAGMAALELMSQRIGWSV 301

Query: 308 Y 308
           +
Sbjct: 302 F 302


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: 317
Number of extensions: 15
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: 302
Length adjustment: 27
Effective length of query: 281
Effective length of database: 275
Effective search space:    77275
Effective search space used:    77275
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