GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Mesorhizobium ciceri WSM1271

Align glutaminase (EC 3.5.1.2) (characterized)
to candidate YP_004142733.1 Mesci_3563 glutaminase, core

Query= BRENDA::P0A6W0
         (308 letters)



>NCBI__GCF_000185905.1:YP_004142733.1
          Length = 315

 Score =  263 bits (673), Expect = 3e-75
 Identities = 148/310 (47%), Positives = 199/310 (64%), Gaps = 6/310 (1%)

Query: 2   AVAMDNAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQER 61
           A  +D A+ E +  ++     +G VA YIP L  VD  + GIA  T DG++  AGDA + 
Sbjct: 7   APKLDRALAE-VAAEMAERTDRGDVASYIPQLGKVDPKKFGIAAVTNDGRVLMAGDADQA 65

Query: 62  FSIQSISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGAL 121
           FSIQSISKV +L +A+ +  +  +WQRVG++PSG+PFNS+VQLE E GIPRNPFINAGA+
Sbjct: 66  FSIQSISKVFTLTLALGNVGDA-LWQRVGREPSGNPFNSIVQLEHENGIPRNPFINAGAI 124

Query: 122 VVCDMLQGRLSAPRQRMLEVVRGLSGVSD---ISYDTVVARSEFEHSARNAAIAWLMKSF 178
           V+ D+L      PR+ + E++R +  ++D   I  D  VA SE     RN A+A  MKSF
Sbjct: 125 VISDILLAG-HQPREAIGEILRFIQFLADDETIIIDREVAASERATGYRNFALANYMKSF 183

Query: 179 GNFHHDVTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALM 238
           GN HH     L  YFH+CA+ MSC +LA    FLAN GK       VV+  +AR+I A+M
Sbjct: 184 GNLHHAPELALGVYFHHCAIAMSCRQLALAGRFLANGGKNPATGHSVVSAERARRIGAMM 243

Query: 239 ATSGMYQNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQ 298
            T G Y  +G+FA+RVG+P KSGVGGGI+ IVP   ++AVWSP L+  GNS  G   LE+
Sbjct: 244 LTCGHYDGSGDFAFRVGIPGKSGVGGGILGIVPGVASLAVWSPGLNANGNSKLGSIALEK 303

Query: 299 LTKQLGRSVY 308
           L + +  S++
Sbjct: 304 LARMMNWSIF 313


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: 277
Number of extensions: 12
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: 308
Length of database: 315
Length adjustment: 27
Effective length of query: 281
Effective length of database: 288
Effective search space:    80928
Effective search space used:    80928
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 24 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