GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Klebsiella michiganensis M5al

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BWI76_RS26540 BWI76_RS26540 D-isomer specific 2-hydroxyacid dehydrogenase family protein

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



>FitnessBrowser__Koxy:BWI76_RS26540
          Length = 317

 Score =  155 bits (392), Expect = 1e-42
 Identities = 100/308 (32%), Positives = 157/308 (50%), Gaps = 17/308 (5%)

Query: 10  LPEDVLA----YLQQHA-QVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLK 64
           LP++++A    YL+    Q++     + +  +  + D DG I    K++  + E A +LK
Sbjct: 7   LPQEIMAEGREYLESRGYQLINGSGMEEEDIIRDIGDCDGIIVRLSKMSDRVFEAAKKLK 66

Query: 65  ALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE-WVKA 123
            ++    G+D  D+    R G+V+ N P   + S A+     +L  +R    + E  ++ 
Sbjct: 67  VVARHGAGYDTVDLESAKRHGVVVLNAPIANSMSVAELAIFYMLHCSRNFKLVQEKMLED 126

Query: 124 GHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAY 183
            +W     P    V++ GKTLG++G+G IG  VA +A  GFNMKV+    + +P   +  
Sbjct: 127 YYWAKLRTPK---VELDGKTLGLIGVGNIGSRVAIKALHGFNMKVI----AYDPYKTQQQ 179

Query: 184 GARRVELAE----LLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239
               VEL +    +   +DFV L  P T ET   +G  +   MK SA  IN +RG  VDE
Sbjct: 180 IPEGVELTDDFDRIFTESDFVSLHCPTTAETTDFVGEKQFSMMKPSAYFINTARGKLVDE 239

Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299
           KAL  AL    I GAG+DV + EP  ++ P+  L+N+V  PHIG+AT E     + ++A 
Sbjct: 240 KALYHALSTHAIAGAGVDVLKKEPFDANDPIFSLSNIVIAPHIGAATIEATDRASLHSAI 299

Query: 300 NLVAALDG 307
            +   L G
Sbjct: 300 GIDEVLSG 307


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: 239
Number of extensions: 17
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: 317
Length adjustment: 28
Effective length of query: 293
Effective length of database: 289
Effective search space:    84677
Effective search space used:    84677
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