GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Shewanella sp. ANA-3

Align glutaminase (EC 3.5.1.2) (characterized)
to candidate 7023976 Shewana3_1184 glutaminase (RefSeq)

Query= BRENDA::P0A6W0
         (308 letters)



>lcl|FitnessBrowser__ANA3:7023976 Shewana3_1184 glutaminase (RefSeq)
          Length = 304

 Score =  391 bits (1005), Expect = e-114
 Identities = 189/303 (62%), Positives = 245/303 (80%), Gaps = 1/303 (0%)

Query: 6   DNAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQ 65
           + A+LE ++ +VRPL+GQGKVA+YIPALA VD  +LGIA+ T+DG+   AGD  E FSIQ
Sbjct: 3   EQALLEEVVDKVRPLLGQGKVANYIPALANVDAGKLGIAVTTIDGETIGAGDYLEPFSIQ 62

Query: 66  SISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCD 125
           SISKV SL +A+  Y E EIW RVGK+PSG  FNSLVQ+E+E+G PRNPFINAGALV+ D
Sbjct: 63  SISKVFSLTLALTLYEETEIWSRVGKEPSGHSFNSLVQVELERGKPRNPFINAGALVIAD 122

Query: 126 MLQGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDV 185
           +LQ RL AP+ RMLE+VR LS    + +D  VA SE++HSARNAAIA+LMKSFGNF  DV
Sbjct: 123 LLQSRLGAPKHRMLELVRALSQNDKVCFDKQVADSEYQHSARNAAIAYLMKSFGNFQGDV 182

Query: 186 TTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQ 245
            TVL+ YFHYCALKM+C +L+R  ++LAN+GK +   E +++ +Q RQ+NAL+ATSG+Y 
Sbjct: 183 DTVLRTYFHYCALKMNCADLSRAMLYLANRGKTLDGTE-LISQVQTRQLNALLATSGLYD 241

Query: 246 NAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGR 305
            AGEFA+RVG+P KSGVGGGI+A++P E+++ VWSPELD+ GNSLAG A+LE L+++LGR
Sbjct: 242 GAGEFAYRVGMPGKSGVGGGIIAVIPGELSVCVWSPELDNQGNSLAGTAMLEHLSQRLGR 301

Query: 306 SVY 308
           S++
Sbjct: 302 SIF 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: 341
Number of extensions: 11
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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