GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Desulfoscipio geothermicus DSM 3669

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase

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



>NCBI__GCF_900115975.1:WP_092482325.1
          Length = 330

 Score =  167 bits (422), Expect = 4e-46
 Identities = 107/325 (32%), Positives = 169/325 (52%), Gaps = 8/325 (2%)

Query: 2   KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGAT 61
           KK++  +++ E+ +  +++ A++        +  + A+ DAD  I  S K+T A++E   
Sbjct: 3   KKVLLTEAIHEEGMNIIREAAELEIAADPGEETVIKAIADADALIVRSSKVTSAIIEAGK 62

Query: 62  RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121
           +LK +    +G D  D+    + G+ + NTPD    S A+ V + +L   +R+ E+   +
Sbjct: 63  KLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLKEVDNAL 122

Query: 122 KAGHWQHSIG-PAL---FGVDVQ---GKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174
           + G +      P L    G   Q   GKTLG+VG+G+I   +A     GF+M+V   +  
Sbjct: 123 RTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQVCGYDAY 182

Query: 175 ANPQAEEAYGARRV-ELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASR 233
             P   +  G      L E+   ADF+ + VPLTP T+ LIG  +L  MK +A LIN++R
Sbjct: 183 LAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAFLINSAR 242

Query: 234 GATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAM 293
           G  V+E  L +AL+  +I GA +DVF  EP   + PL  L NVV  PHI + T      M
Sbjct: 243 GGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTDGALVRM 302

Query: 294 ARNAAENLVAALDGTLTSNIVNREV 318
           AR+ AE +V+ L G     +VN  +
Sbjct: 303 ARDVAEGVVSVLRGERPKYLVNPRI 327


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: 234
Number of extensions: 16
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: 330
Length adjustment: 28
Effective length of query: 293
Effective length of database: 302
Effective search space:    88486
Effective search space used:    88486
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