GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-aldolase in Salinicoccus carnicancri Crm

Align Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE; KDG aldolase YagE; Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE; EC 4.1.2.51; EC 4.1.2.28 (characterized)
to candidate WP_017549000.1 C792_RS0108265 4-hydroxy-tetrahydrodipicolinate synthase

Query= SwissProt::P75682
         (302 letters)



>NCBI__GCF_000330705.1:WP_017549000.1
          Length = 297

 Score =  135 bits (340), Expect = 1e-36
 Identities = 80/245 (32%), Positives = 135/245 (55%), Gaps = 4/245 (1%)

Query: 4   SALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFSQLGAEERKA 63
           + +F GI   ++T F  D  +D       I+ LI+     L   G+ GE   L AEE + 
Sbjct: 3   TVIFEGIGVAMTTPFRND-VIDYGAFRNHIEYLIENDAQALIINGTTGESPTLRAEEIRE 61

Query: 64  IARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADGIVVINPYYWKVSEANLIRY 123
           + R  ++ VD RVPV+ GTG  +   +IEL+++A++ GAD I++I PYY K ++  LIR+
Sbjct: 62  LLRVGVETVDGRVPVIAGTGTNSTSASIELTKYAEKIGADAIMLITPYYNKSNQRGLIRH 121

Query: 124 FEQVADSVTLPVMLYNFPALTGQDLTPALVKTLADSRSNIIGIKDTIDSVAHLRSMIHTV 183
           F  +AD+  LP +LYN P  TG  + P  V+ L+  R NI+ +KD +  + + R ++   
Sbjct: 122 FTAIADNTELPAVLYNVPGRTGMTIEPETVRELSTHR-NIVALKDAVGDLEYTREVLALT 180

Query: 184 KGAHPHFTVLCGYDDHLFNTLLLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQ 243
           +  +  F +  G DD++ + + LGG G IS  GN  P    ++ +  ++GD +    +++
Sbjct: 181 E--NQDFVLYSGNDDNMHDFVKLGGKGLISVVGNIIPGELQDVYERIQNGDASAQDRFNR 238

Query: 244 TLLQI 248
            +  I
Sbjct: 239 VMPMI 243


Lambda     K      H
   0.320    0.138    0.407 

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: 189
Number of extensions: 10
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: 302
Length of database: 297
Length adjustment: 27
Effective length of query: 275
Effective length of database: 270
Effective search space:    74250
Effective search space used:    74250
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 (21.8 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