GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Phaeobacter inhibens BS107

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2783 PGA1_c28260 glyoxylate reductase GyaR

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



>FitnessBrowser__Phaeo:GFF2783
          Length = 328

 Score =  177 bits (450), Expect = 2e-49
 Identities = 124/311 (39%), Positives = 168/311 (54%), Gaps = 9/311 (2%)

Query: 4   IVAWKSLPEDVLAYLQQHAQV-VQVDAT--QHDAFVAALKDADGGIGSSVKITPAMLEGA 60
           +V  + LPE V   L +   V ++ D T         ALKDAD  + +      A L G 
Sbjct: 8   VVVTRRLPEPVETRLSELFDVRLREDDTPMSRAELATALKDADVLVPTVTDEIDAGLLGQ 67

Query: 61  T--RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118
              RLK ++    G D  DVA   +RGI+++NTP VLT+ TAD   +LI+A  RR+ E  
Sbjct: 68  AGDRLKLIANYGAGVDHIDVATARQRGILVSNTPGVLTDDTADMAMALIMAVVRRIPEGL 127

Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTN-RSANP 177
             ++ G WQ     AL G  + G+ LGI+G+G IG AVA+RAA  F M+V Y N R   P
Sbjct: 128 AVMQKGDWQGWSPTALLGGRLAGRRLGILGMGSIGQAVAKRAA-AFGMQVHYHNRRRLRP 186

Query: 178 QAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGAT 236
           + E+ + A   E L +++A  D + +  P TP T HL+ A  LK MK  A+++N SRG  
Sbjct: 187 EIEQRFEATYWESLDQMVARMDVLSINCPSTPSTFHLMNARRLKLMKPDAVIVNTSRGEV 246

Query: 237 VDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARN 296
           +DE AL   L+   I GAGLDV+E      +  L +L NVV LPH+GSAT E R  M   
Sbjct: 247 IDEHALTRMLRASEIAGAGLDVYE-HGTDINPRLRELENVVLLPHMGSATLEGRLEMGEK 305

Query: 297 AAENLVAALDG 307
              N+    DG
Sbjct: 306 VLLNIKTFEDG 316


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: 241
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: 321
Length of database: 328
Length adjustment: 28
Effective length of query: 293
Effective length of database: 300
Effective search space:    87900
Effective search space used:    87900
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: 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