GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Porphyrobacter dokdonensis DSW-74

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_068863251.1 I603_RS04065 phosphoglycerate dehydrogenase

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>NCBI__GCF_001677335.1:WP_068863251.1
          Length = 528

 Score =  183 bits (464), Expect = 9e-51
 Identities = 111/320 (34%), Positives = 170/320 (53%), Gaps = 5/320 (1%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGA 60
           K +++ K  P     + ++   V  +     +  +A + + DG  I SS K+T A+L+ A
Sbjct: 5   KVLISDKMDPNAARIFEERGCDVDVITGETPEQLIARIGEYDGLAIRSSTKVTKAVLDAA 64

Query: 61  TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120
           T LK +    +G D  D+   + +G+V+ NTP   + +TA+   +L+ A AR++ +    
Sbjct: 65  TNLKVIGRAGIGVDNVDIPYASSKGVVVMNTPFGNSITTAEHAIALMFALARQIPDANAQ 124

Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180
            +AG W  S      GV++  KTLG++G G IG  VA RA LG  MKV+  +        
Sbjct: 125 TQAGLWPKS---GFMGVELTNKTLGLIGAGNIGSIVASRA-LGLRMKVIAYDPFLTEDRA 180

Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240
              G  +V+L  LL+ ADFV L  PLT ET++++    L+  KK   +IN +RG  +DE 
Sbjct: 181 VEMGVEKVDLDTLLSRADFVTLHTPLTEETRNILSRERLEGAKKGIRIINCARGGLIDEA 240

Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300
           AL + L++G + GA LDVFETEP   D PL    N +  PH+G++T E +  +A   AE 
Sbjct: 241 ALRDCLESGQVAGAALDVFETEPPAKDHPLFGTPNFICTPHLGASTTEAQVNVALQVAEQ 300

Query: 301 LVAALDGTLTSNIVNREVLS 320
           L   L     +N +N   LS
Sbjct: 301 LSDYLVNGGVTNALNVPSLS 320


Lambda     K      H
   0.317    0.131    0.366 

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: 346
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: 321
Length of database: 528
Length adjustment: 31
Effective length of query: 290
Effective length of database: 497
Effective search space:   144130
Effective search space used:   144130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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