GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ketodeoxyribonate-cleavage in Phaeobacter inhibens BS107

Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate GFF826 PGA1_c08400 Uncharacterized conserved protein

Query= reanno::WCS417:GFF1426
         (310 letters)



>FitnessBrowser__Phaeo:GFF826
          Length = 305

 Score =  165 bits (418), Expect = 1e-45
 Identities = 114/328 (34%), Positives = 160/328 (48%), Gaps = 49/328 (14%)

Query: 1   MSKNRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRP 60
           M+KN  V ITCAVTG+  T   SPH+P + + IA++AI AA+AGAAIVH H RDP  G P
Sbjct: 5   MAKN--VFITCAVTGSGSTQDRSPHVPRSPKAIAESAIAAAKAGAAIVHCHVRDPETGAP 62

Query: 61  SQDPALFAEFLPQIKAA-SDVVINITTG-------------------GAPTMGVEERLQP 100
           S+D  L+ E   +I+ + +DVV+N+T G                   G   +G   R+  
Sbjct: 63  SRDLTLYREVTDRIRESDTDVVLNLTAGMGGDMVFGDTENPLPLNEAGTDMIGATARMAH 122

Query: 101 VMQFKPELASLNMGSMNFGLYEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNA 160
           V +  PE+ +L+ G+MNF                         D +  NT   +  +   
Sbjct: 123 VAECLPEICTLDCGTMNFA----------------------EADYVMTNTPGMLRAMGQM 160

Query: 161 CAENRTRFEIECYDIGHLYTAAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTA 220
             +   + EIE +D GHL+ A   ++ G+L  P  +Q   G+  G    P DL       
Sbjct: 161 MTDLGVKPEIEAFDTGHLWFAKELVKEGVLNSPALVQLCMGVPWGA---PNDLNTFMAMV 217

Query: 221 DRLFGSDYVWSILGAGRGQIPLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIR 280
           + +  SD+ WS    GR Q+      +  G N RVGLED+LW G G+L A N   V R  
Sbjct: 218 NNV-PSDWDWSAFSLGRDQMAYVAASVLAGGNVRVGLEDNLWLGKGQL-AENWQLVERAG 275

Query: 281 TVIEALGHRVATPDEAREILGLKGRDQV 308
           T+IE +G ++  PDE R  LGL  R  V
Sbjct: 276 TIIENMGAKLMGPDEVRAQLGLVKRAPV 303


Lambda     K      H
   0.321    0.138    0.416 

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: 282
Number of extensions: 13
Number of successful extensions: 5
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: 310
Length of database: 305
Length adjustment: 27
Effective length of query: 283
Effective length of database: 278
Effective search space:    78674
Effective search space used:    78674
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