GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Methanosarcina acetivorans C2A

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_011021352.1 MA_RS06920 NAD(P)-dependent oxidoreductase

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



>NCBI__GCF_000007345.1:WP_011021352.1
          Length = 319

 Score =  195 bits (496), Expect = 1e-54
 Identities = 120/289 (41%), Positives = 164/289 (56%), Gaps = 9/289 (3%)

Query: 33  DAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTP 92
           D F+  +KDAD  +     ++   L  A RLK +S    GFD  D+ + T  G++++N P
Sbjct: 36  DEFIDRIKDADIVVVGRYGVSAEALRSAPRLKMISLWQTGFDNVDLEEATDHGVIVSNVP 95

Query: 93  DVLTESTADTVFSLILASARRVVELAEWVKAG--HWQHSIGPALFGVDVQGKTLGIVGLG 150
               ES A+ VF+L L   RRV      ++ G   W++ +G  L       KT+G++G G
Sbjct: 96  SYAFESVAEFVFALTLNLLRRVHLADMNLREGLFDWKYYVGNQLMS-----KTIGVLGTG 150

Query: 151 RIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPET 210
            IG  V +  A GFNM VL      +P+  +A G + V+L  LL+ +D V L VPLTPET
Sbjct: 151 EIGKRVIQ-IAHGFNMNVLSVTAHPSPERAKALGVKFVDLDTLLSESDIVTLHVPLTPET 209

Query: 211 KHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPL 270
           +H+IGA EL  MK +AILIN +RG  V+E AL+EAL+   I GAGLDVFE EPL  DSPL
Sbjct: 210 EHMIGARELAKMKPTAILINTARGKVVEEAALMEALKEKKIAGAGLDVFEREPLSMDSPL 269

Query: 271 LKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNREVL 319
           L++ NVV  PHI   + E+       + EN+     G    N+VN  VL
Sbjct: 270 LEMHNVVLTPHIAFLSEESLDECTYISIENVEMFAKGK-PQNVVNPSVL 317


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: 218
Number of extensions: 9
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: 319
Length adjustment: 28
Effective length of query: 293
Effective length of database: 291
Effective search space:    85263
Effective search space used:    85263
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 Apr 09 2024. 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