GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Shewanella oneidensis MR-1

Align glutaminase (EC 3.5.1.2) (characterized)
to candidate 202473 SO3365 glutaminase A (NCBI ptt file)

Query= BRENDA::P0A6W0
         (308 letters)



>FitnessBrowser__MR1:202473
          Length = 304

 Score =  390 bits (1002), Expect = e-113
 Identities = 188/303 (62%), Positives = 245/303 (80%), Gaps = 1/303 (0%)

Query: 6   DNAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQ 65
           + A+LE ++ +VRPL+GQGKVA+YIPALA +D  +LGIA+ T+DG+   AGD  E FSIQ
Sbjct: 3   ETALLEEVVDRVRPLLGQGKVANYIPALANIDPGKLGIAVTTIDGETIGAGDYLEPFSIQ 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++  ++LAN+GK +   E +++ +Q RQ+NAL+ATSG+Y 
Sbjct: 183 DTVLRTYFHYCALKMNCADLSKAMLYLANRGKTLDGTE-LISQVQTRQLNALLATSGLYD 241

Query: 246 NAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGR 305
            AGEFA+RVG+P KSGVGGGI+A++P E+++ VWSPELD  GNSLAG A+LEQL+++LGR
Sbjct: 242 GAGEFAYRVGMPGKSGVGGGIIAVIPGELSVCVWSPELDTQGNSLAGTAMLEQLSQRLGR 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: 334
Number of extensions: 8
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