GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Oceanisphaera arctica V1-41

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_104487446.1 UN63_RS13580 D-2-hydroxyacid dehydrogenase

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



>NCBI__GCF_002936955.1:WP_104487446.1
          Length = 316

 Score =  143 bits (360), Expect = 6e-39
 Identities = 99/276 (35%), Positives = 137/276 (49%), Gaps = 14/276 (5%)

Query: 39  LKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTES 98
           L+D D  I + V++   +L    RLK +   + G D  D+    + GI + N  D    S
Sbjct: 41  LQDTDIAIVNKVRLGADILSRLPRLKLVVIAATGSDNVDLEACRQAGIAVCNIRDYSKNS 100

Query: 99  TADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV---DVQGKTLGIVGLGRIGGA 155
             +   +LILA  R +      + AG WQ S     F     D+ G+TLG++G G I   
Sbjct: 101 VPEHALALILALNRSLNAYRASIVAGRWQQSGQFCYFDYPVRDLAGQTLGLIGYGTIARE 160

Query: 156 VARRA-ALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLI 214
           + + A ALG  MKV+   R  +P +E      RV   +LL  AD + L  PL  ET+HLI
Sbjct: 161 LEKLATALG--MKVIVAARKGHPVSEG-----RVGFEQLLNDADVISLHCPLNAETRHLI 213

Query: 215 GAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPL---L 271
           G  ELK MK  A+L+N  RG  VDE AL+ AL+   I GAG DV   EP   D+PL   L
Sbjct: 214 GERELKLMKSDALLVNVGRGGLVDEAALLAALEQNRIGGAGFDVVTQEPPAPDNPLMQAL 273

Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
           +  N +  PHI  A+      +A    +N+ A + G
Sbjct: 274 QYPNFILTPHIAWASRNAMQRLADQLIDNIEAFVAG 309


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: 214
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: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
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 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