GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Cronobacter universalis NCTC 9529

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_038858516.1 AFK65_RS00065 2-hydroxyacid dehydrogenase

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



>NCBI__GCF_001277175.1:WP_038858516.1
          Length = 310

 Score =  169 bits (427), Expect = 1e-46
 Identities = 126/311 (40%), Positives = 173/311 (55%), Gaps = 21/311 (6%)

Query: 1   MKKIVAWKS-LPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEG 59
           MK IV   + LP+ + A L++   + +        FVA      G I + V    A++ G
Sbjct: 1   MKTIVLKHAYLPDALTAELRERYDLREFSQMSDADFVAIA----GDIAALVTNGEAVVTG 56

Query: 60  A--TRLKALSTISV---GFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRV 114
               RL ALS I+V   G+D  DVA    RGI + +TP VLT+  AD    L+LA++RR+
Sbjct: 57  EFIARLPALSLIAVFGVGYDGVDVAAALERGIAVTHTPGVLTDDVADLAIGLMLATSRRI 116

Query: 115 VELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174
           V   ++++ G WQ   G   +   V G  LGI G+GRIG A+ARRA   F+M + YT R 
Sbjct: 117 VAAQKFIEQGGWQQ--GGFTWTRKVSGARLGIFGMGRIGQAIARRAQ-AFDMTISYTGR- 172

Query: 175 ANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASR 233
              Q   A   R V  LA+L   +DF+ L  P    T+ ++ AA L+++    ILIN +R
Sbjct: 173 ---QPHSALPYRFVPGLAQLAQESDFLMLCAPGGDATRGVVNAAVLEALGPQGILINIAR 229

Query: 234 GATVDEKALIEALQNGTIHGAGLDVFETEP-LPSDSPLLKLANVVALPHIGSATHETRHA 292
           G+ VDE ALI AL++G I GAGLDVF  EP +P+   L +  NVV  PH+ SAT ETR  
Sbjct: 230 GSVVDEAALIAALESGAIAGAGLDVFTDEPNVPAS--LQQRDNVVITPHMASATRETRRE 287

Query: 293 MARNAAENLVA 303
           M+R   EN+ A
Sbjct: 288 MSRLVLENVNA 298


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: 229
Number of extensions: 12
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: 310
Length adjustment: 27
Effective length of query: 294
Effective length of database: 283
Effective search space:    83202
Effective search space used:    83202
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