GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolJ in Caldicellulosiruptor hydrothermalis 108

Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate WP_013402102.1 CALHY_RS00635 class II fructose-bisphosphate aldolase

Query= curated2:Q5WKY5
         (293 letters)



>NCBI__GCF_000166355.1:WP_013402102.1
          Length = 278

 Score =  175 bits (443), Expect = 1e-48
 Identities = 104/279 (37%), Positives = 156/279 (55%), Gaps = 5/279 (1%)

Query: 4   VPMAPLLADAKKDSYAIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGFQTV 63
           V +  +L+  K   + +G FN     + + ++  AE  + P+I   +DR +D L  F+ +
Sbjct: 3   VNLNEVLSYTKVKKFGVGMFNGLSADFYEGLIDAAEQLRCPIIIGVADRFVDRLD-FEMI 61

Query: 64  VAMMGALTDELGITVPVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINENIDMTKEV 123
             +M  L      +VPV +HLDH  S++   +A+ AGF+SVMFDGS  P  ENI  TKE+
Sbjct: 62  AEVMIFLAKRA--SVPVCVHLDHAKSLKNIMRAIKAGFTSVMFDGSSLPFEENIKRTKEI 119

Query: 124 VAYAHAHNVSVEGEVGTVGGMEDGLMAEIKYADVEECQRFVCETNVDALAAALGSVHGKY 183
           V  AH+  VSVEGE+G VG  +        Y   +E + F  +T VDALA ++G+VHG Y
Sbjct: 120 VEIAHSVGVSVEGELGVVGRGDFDFKNPEFYTKPDEAEEFAQKTQVDALAVSIGTVHGVY 179

Query: 184 KGEPKLGFNEMAAISASTNVPLVLHGASGIPDEQLQRAIKLGHAKININTECMIAWSDAC 243
           KGEPKL F  ++ I    +  LVLHG SG+ DE  ++ I+ G  K+NI T+  +A  +A 
Sbjct: 180 KGEPKLDFERLSEIRKRVDCYLVLHGGSGLSDEDFKKCIEYGINKVNIFTDLTLA-INAQ 238

Query: 244 RTTFAEQETAFEPRLLLQEGLAMVQATVEKKIKQFGAAN 282
              F +Q     P  + ++   +V+    KK+K FG+ N
Sbjct: 239 LPEFIKQTEDLTP-AIFEKIREIVKQEAIKKLKIFGSYN 276


Lambda     K      H
   0.317    0.132    0.378 

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: 184
Number of extensions: 10
Number of successful extensions: 4
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: 293
Length of database: 278
Length adjustment: 26
Effective length of query: 267
Effective length of database: 252
Effective search space:    67284
Effective search space used:    67284
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