GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Rhizobium freirei PRF 81

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate WP_004110704.1 RHSP_RS06210 4-hydroxy-2-oxoheptanedioate aldolase

Query= SwissProt::P23522
         (256 letters)



>NCBI__GCF_000359745.1:WP_004110704.1
          Length = 268

 Score =  246 bits (629), Expect = 3e-70
 Identities = 122/250 (48%), Positives = 170/250 (68%), Gaps = 1/250 (0%)

Query: 8   NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67
           N FK AL   + QIG W AL+N  + E+   AG+DWL+LD EHAPND+   + QL A+KG
Sbjct: 6   NLFKQALKEGRAQIGLWQALANAYTVEISAGAGYDWLLLDAEHAPNDVPLLVSQLQAMKG 65

Query: 68  SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS- 126
           +AS  ++R P  E  IIK++LDIG    LIP V++KE AE  V + RYPP G+RGV  + 
Sbjct: 66  TASHAIIRPPIGETWIIKQMLDIGAQTLLIPMVDSKETAETMVKAVRYPPHGVRGVGAAL 125

Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186
            RA+ F  + DY   +N  I +L+Q+ES+ G++ +DAIA+T+GVDG+F+GP+DLAA +G+
Sbjct: 126 ARASAFNRIPDYLPTANDEICLLLQVESRAGLEALDAIASTDGVDGVFIGPADLAADMGY 185

Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246
           LG    P+VQ  ++    +  AHGK +GIL    + A+RYLE GATFVA+G+D+ +  +A
Sbjct: 186 LGKPGAPEVQAEVEKALAKIQAHGKAAGILIGDLSLAKRYLELGATFVAIGNDVTLLANA 245

Query: 247 TQKLADTFKK 256
           T KL D FKK
Sbjct: 246 TTKLLDDFKK 255


Lambda     K      H
   0.318    0.134    0.392 

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: 208
Number of extensions: 4
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: 256
Length of database: 268
Length adjustment: 25
Effective length of query: 231
Effective length of database: 243
Effective search space:    56133
Effective search space used:    56133
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: 47 (22.7 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