GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Cronobacter condimenti 1330

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_007680625.1 BN137_RS02000 glyoxylate/hydroxypyruvate reductase GhrB

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



>NCBI__GCF_000319285.1:WP_007680625.1
          Length = 325

 Score =  336 bits (861), Expect = 5e-97
 Identities = 176/321 (54%), Positives = 225/321 (70%), Gaps = 3/321 (0%)

Query: 4   IVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVA---ALKDADGGIGSSVKITPAMLEGA 60
           ++ +KSLP+D+LA L+ H  V +V         A   A   A G +GSS K+  A+LE  
Sbjct: 5   VILYKSLPDDLLARLESHFSVTRVSDLSPQTVAAHAQAFSQAQGLLGSSEKVDAALLEKM 64

Query: 61  TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120
             L+A ST+SVG+D FDV  L  + I L +TP VLTE+ ADT+ +L+L +ARR +E+A+ 
Sbjct: 65  PALRATSTVSVGYDNFDVDALNAKQIALMHTPTVLTETVADTLMTLVLTTARRALEVADR 124

Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180
           VKAG W  SIGP  FG+DV  KTLGI+G+GRIG A+A+RA  GFNM +LY  R  + +AE
Sbjct: 125 VKAGEWTGSIGPDWFGIDVHHKTLGIIGMGRIGLALAQRAHFGFNMPILYNARRHHSEAE 184

Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240
           E + AR  ++  LLA +DFVC+ +PLT ET H+IGA + + MKKSAI INA RG  VDE 
Sbjct: 185 ERFNARYCDIDTLLAESDFVCVILPLTDETHHMIGAEQFRKMKKSAIFINAGRGPVVDEN 244

Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300
           ALI ALQ+G IH AGLDVFE EPLP DSPLL L NVVALPHIGSATHETR+ MA  A +N
Sbjct: 245 ALISALQSGEIHAAGLDVFEQEPLPKDSPLLSLKNVVALPHIGSATHETRYNMAACAVDN 304

Query: 301 LVAALDGTLTSNIVNREVLSK 321
           L+ AL+G ++ N VN +V+ K
Sbjct: 305 LINALNGDVSQNCVNPQVVKK 325


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: 244
Number of extensions: 3
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: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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