GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Phaeacidiphilus oryzae TH49

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate WP_084703970.1 BS73_RS11395 5-dehydro-2-deoxygluconokinase

Query= reanno::HerbieS:HSERO_RS12125
         (657 letters)



>NCBI__GCF_000744815.1:WP_084703970.1
          Length = 385

 Score =  169 bits (427), Expect = 3e-46
 Identities = 119/347 (34%), Positives = 171/347 (49%), Gaps = 19/347 (5%)

Query: 22  DLICIGRLAVDLYAQQVGAPLSDVSSFAKYLGGSSANIAFGCARLGLKSAMLARIGDEAN 81
           DLI +GR+ VD+Y  Q+G PL++V +F K+LGGS+ N+A   ARL  +SA+++R G +  
Sbjct: 21  DLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGADPF 80

Query: 82  GQFLKAELAAEGCDVSHVTVDPQRLTALVMLGLKDKDSFPLIFY-RDNCADMALAPEDID 140
           G+++   L   G D   VT   +  T +    +   D FP+ FY R    D+ + PE++D
Sbjct: 81  GEYVHRALREFGVDDRWVTPVQRYPTPVTFCEIFPPDDFPIWFYRRPKAPDLEIHPEELD 140

Query: 141 EAFIASSKALLITGTHF--STPQVHRSSSLALQYARRHNVRTVLDIDYRPVLWGLTSKGD 198
              I S+    ITGT       +    ++LA + AR     TV D+D+RP  WG    G+
Sbjct: 141 LDAIRSAGIFWITGTGLCEEPSRTATLAALAARSARPGAGPTVFDLDWRPAFWG----GE 196

Query: 199 GETRFIASDGVTQHLQGILPQF-------DLVVGTEEEFMIAGGSTDIMAALRAVRALCA 251
           G       +G  + +    P +        + VG  +E  +A G  D  A   A+  L A
Sbjct: 197 GGASGDGGEGGARAMAEARPIYREALAHATVAVGNLDEAEVATGLRDPQACAEALLELGA 256

Query: 252 ATLVVKRGPLGCVVLHGAIPERLDDGFHYRGVQVEVLNVLGAGDAFISGFLKGWLNEEDD 311
              VVK+GP G + LH     R         V VEV+N LGAGDAF      G L     
Sbjct: 257 ELAVVKQGPKGVLALH-----RDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPL 311

Query: 312 EHCCRYANACGALVVSRHACAPAMPGPIELDYFLQHAHRLQRPDRDA 358
           E   R+ANA GA+V  R AC+ AMP P E++  L        P+ +A
Sbjct: 312 ERTVRWANAAGAIVAGRLACSSAMPTPEEIEQRLTETETRADPETEA 358


Lambda     K      H
   0.322    0.137    0.414 

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: 582
Number of extensions: 28
Number of successful extensions: 5
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: 657
Length of database: 385
Length adjustment: 34
Effective length of query: 623
Effective length of database: 351
Effective search space:   218673
Effective search space used:   218673
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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