GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Marivita geojedonensis DPG-138

Align gluconate/galactonate dehydratase (EC 4.2.1.140); gluconate dehydratase (EC 4.2.1.39) (characterized)
to candidate WP_085636267.1 MGEO_RS08380 mandelate racemase/muconate lactonizing enzyme family protein

Query= BRENDA::Q6L1T2
         (391 letters)



>NCBI__GCF_002115805.1:WP_085636267.1
          Length = 411

 Score =  195 bits (496), Expect = 2e-54
 Identities = 130/386 (33%), Positives = 198/386 (51%), Gaps = 27/386 (6%)

Query: 15  PGEKSSPWSSTILIVKLTSSNGNIGYGEAPTTFMTLPVKESMRE--VERVFKDQNYFNIE 72
           PG     W+     VK+T+  G  G+GE   + +     +++ E   +R  K +N  NIE
Sbjct: 16  PGWGGRYWT----FVKVTTDTGITGWGECYASSVGPTAMKAVIEDVFDRHMKGENPENIE 71

Query: 73  KNMREFYKHSFYLSRSMEATSALSAFEIASWDLIGKDLGTPVYNLLGGEYNSELRAYA-- 130
              R  Y   F     +    A S  EIA WD++GK    PV+ LLGG  N  +RAY   
Sbjct: 72  LMFRRAYSSGFTQRPDLTVMGAFSGLEIACWDILGKARNRPVWALLGGRMNERVRAYTYL 131

Query: 131 --------NGWYSDCLEPDDFVSRAKEYIKKGYTAFKFDPFRNNFDRIGND----GIKKA 178
                   N +++D   PD     AKEY+++G+TA KFDP        G+      +  +
Sbjct: 132 YPLPHHDLNSFWTD---PDAQAEAAKEYVRQGFTALKFDPAGPYTIHGGHQPALTDVSLS 188

Query: 179 VDIVSAMRSELGENIDLLIECHGRFSTKYAIKVGQALDEFNPLFIEEPIHPEMELGLFDF 238
           V++  A+R+ +G+  DLL   HG+F+T  AI++GQA++ + PL+ EEPI P+  L   + 
Sbjct: 189 VEMCKAIRAAVGDRADLLFGTHGQFTTSGAIRLGQAIEPYLPLWYEEPIPPDNLLEFAEV 248

Query: 239 KRYVNTPVALGERLLNKEDFARYISQGMVDIVQADLTNSKGILEAKKISAIVESFGGLMA 298
            R V  P+A GER+  K +FA  +  G   I+Q  L  + GI E KK++A+ E+F   MA
Sbjct: 249 ARAVRIPIATGERMTTKAEFATLLRTGGAKILQPALGRAGGIWEMKKLAAMAEAFNAEMA 308

Query: 299 FHNAFGPVQTAATLNVDYTLTNFLIQESFEDSWPDWKRNLFSGYRIENGHFKLSGKPGLG 358
            H   GPV+ AA +++  ++ N LI E+ E   P     + +  R+E+G+      PGLG
Sbjct: 309 PHLYAGPVEWAANIHLCASIPNVLIAETIET--PFHAALIRNSIRVEDGYITPPETPGLG 366

Query: 359 ITADEKLMEKLIY--DGMEEFNKNEP 382
           I  DE+      +  DG+    +NEP
Sbjct: 367 IEFDEEFARAHPFTGDGLHLQMQNEP 392


Lambda     K      H
   0.317    0.136    0.401 

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: 366
Number of extensions: 27
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: 391
Length of database: 411
Length adjustment: 31
Effective length of query: 360
Effective length of database: 380
Effective search space:   136800
Effective search space used:   136800
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 (21.6 bits)
S2: 50 (23.9 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