GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Limnohabitans curvus MWH-C5

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_094478843.1 B9Z44_RS12305 hydroxyacid dehydrogenase

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



>NCBI__GCF_003063475.1:WP_094478843.1
          Length = 337

 Score =  149 bits (376), Expect = 9e-41
 Identities = 107/320 (33%), Positives = 164/320 (51%), Gaps = 22/320 (6%)

Query: 1   MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQ---HDAFVAALKDADGGIGSSV-KITPAM 56
           M KIV  + + E VLA L+    VV     +    +     LKDAD  +     ++    
Sbjct: 2   MPKIVVTQPIHEAVLARLRSAGDVVMNQGPEPWSEEELYLHLKDADAMMAFMPDRVDMRT 61

Query: 57  LEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVE 116
           L  A RLK ++    G+D FD+    + G+ ++  PD+LTE TA+    L +A+AR V+ 
Sbjct: 62  LLNAPRLKTIACALKGYDNFDLMACEKAGVSVSFVPDLLTEPTAELAIGLAIAAARHVLA 121

Query: 117 LAEWVKAGH--WQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174
               V+ G+  W+    P L+G+ + G  + +VGLG +G A+  R   GF    L     
Sbjct: 122 GDTRVRRGYAGWR----PQLYGIGLHGSVVSVVGLGAVGRAIVDRLC-GFGCAQLL---G 173

Query: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234
            +P  ++      V L E L+ +D+V L VPL   T+HL+    L+ +++  IL+N  RG
Sbjct: 174 VDPHGDDER-LTMVSLGEALSQSDYVILAVPLLDVTRHLVNDTMLEGVRRGQILVNIGRG 232

Query: 235 ATVDEKALIEALQNGTIHGAGLDVFETEP-LPSDSP------LLKLANVVALPHIGSATH 287
           + VDE A+  AL++  +     DV+E E  L +D P      LL+  + V  PHIGSA  
Sbjct: 233 SVVDEAAVARALKDERLGAYAADVYEMEDWLLADRPRQIHPELLQHPSTVFTPHIGSAVK 292

Query: 288 ETRHAMARNAAENLVAALDG 307
           + R A+   AAENL+ AL+G
Sbjct: 293 KVRRAIELQAAENLLVALNG 312


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: 233
Number of extensions: 14
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: 337
Length adjustment: 28
Effective length of query: 293
Effective length of database: 309
Effective search space:    90537
Effective search space used:    90537
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: 49 (23.5 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