GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate H281DRAFT_02329 H281DRAFT_02329 dihydroxyacid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Burk376:H281DRAFT_02329
          Length = 577

 Score =  772 bits (1993), Expect = 0.0
 Identities = 381/571 (66%), Positives = 455/571 (79%), Gaps = 2/571 (0%)

Query: 9   RKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAE 68
           + LRSQ W+G   RD   HR W+KNQG PHD FDGRPVIGI NTWS++TPCN H RELAE
Sbjct: 9   KPLRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRELAE 68

Query: 69  KVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCD 128
            VK GV EAGG PLE PV S  E   RPTAM++RNLA++ VEE+IRG PMDG +LLVGCD
Sbjct: 69  YVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLVGCD 128

Query: 129 KTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLE 188
           KTTP+LLMGAASC+LP++ V+GGPMLNG FRG+ +GSGT +W+ SE V+AG MTQ EF E
Sbjct: 129 KTTPALLMGAASCNLPALAVSGGPMLNGRFRGKHIGSGTGVWQMSEEVRAGSMTQEEFTE 188

Query: 189 AEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMV 248
           AE+ M+RS G C TMGTASTMASM E+LGM L  NAAIP VD+RR+V+A L GRRIV MV
Sbjct: 189 AESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIVDMV 248

Query: 249 KDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPT 308
           ++DL   +I+T+QAFENAIRTNAAIGGSTNAV+HL+A+A R+G++LSL+DW+  G +VP 
Sbjct: 249 REDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDWE-LGSNVPC 307

Query: 309 IVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDV 368
           +VNL PSG+YLME+F+YAGGLP VLK+LGE GLLH++ALTV+G+T+WD V++  N +E V
Sbjct: 308 LVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHREALTVNGKTIWDNVRNAPNHDEKV 367

Query: 369 ILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDD 428
           I    +      GI VL+GNLAP GAV+KPSAA+  LL H+GRAVVFE+I++  AKI+D+
Sbjct: 368 ITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATAELLKHRGRAVVFENIEELHAKIDDE 427

Query: 429 NLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVV 488
           +LDIDENCIMV+K  GPKGYPG AEVGNM LP KVL+KGI DMVRISD RMSGTAYG VV
Sbjct: 428 SLDIDENCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYGAVV 487

Query: 489 LHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAF 548
           LH SPEAA GGPLA V+ GDMIELDV  RRLHLD+SD+ELARR A WQ   + P  GY  
Sbjct: 488 LHVSPEAAAGGPLAFVQTGDMIELDVEARRLHLDVSDDELARRRAAWQA-PESPKRGYYK 546

Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
           L+ +HV  AD GADLDFL G  G  V +DSH
Sbjct: 547 LYVEHVLQADQGADLDFLVGSSGAPVPRDSH 577


Lambda     K      H
   0.318    0.135    0.408 

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: 1147
Number of extensions: 60
Number of successful extensions: 3
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: 579
Length of database: 577
Length adjustment: 36
Effective length of query: 543
Effective length of database: 541
Effective search space:   293763
Effective search space used:   293763
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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