GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Dinoroseobacter shibae DFL-12

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 3606698 Dshi_0129 dihydroxy-acid dehydratase (RefSeq)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Dino:3606698
          Length = 577

 Score =  308 bits (788), Expect = 5e-88
 Identities = 204/576 (35%), Positives = 304/576 (52%), Gaps = 30/576 (5%)

Query: 1   MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60
           M K++    KL S+    G SR    HR +    G   +    +P++G+   W++  PCN
Sbjct: 1   MLKRSFDKSKLPSRHVTEGPSRAP--HRSYYYAMGMTEEEIH-QPLVGVATCWNEAAPCN 57

Query: 61  GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLA-----ALAVEEAIRG 115
             L   A+ VK GV +A G P E    + ++        M  +LA     A  VE  +RG
Sbjct: 58  IALSRQAQAVKMGVKQASGTPREFTTITVTDGIAMGHEGMRSSLASREAIADTVELTMRG 117

Query: 116 QPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEM 175
              D  V L GCDK+ P ++M     ++PS+ + GG +L G   GE V +   +++    
Sbjct: 118 HCYDAIVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPGRLNGEDV-TVQDVFEAVGK 176

Query: 176 VKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKV 235
            +AG  T AE    E     S+G C    TA+TMA ++EA+G+AL  +A  P     R  
Sbjct: 177 HQAGNYTDAELEVLERVACPSAGACGGQFTANTMACVSEAIGLALPNSAGAPAPYESRDQ 236

Query: 236 MAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLS 295
             + +GR ++ +++  ++  +I+T+++ ENA R  A  GGSTNA +HL AIA   GI+ +
Sbjct: 237 YGEASGRAVMDLIEKGIRARDIVTRKSLENAARIVACTGGSTNAGLHLPAIAHEAGIEFT 296

Query: 296 LDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVW 355
           L D     RD P  V+L P GKY+ ++ + AGG+PVV++ L  AGL+H+D +TV+G ++ 
Sbjct: 297 LQDVCDIFRDTPYFVDLKPGGKYVAKDMYEAGGVPVVMRELRRAGLIHEDCMTVTGYSIG 356

Query: 356 DEVKDVVNWNED--VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAV 413
           +E+ D V    D  VI P +  L+++GG+V L GNLAP+GA++K +  S   LV  G A 
Sbjct: 357 EEL-DKVTLEADGRVIYPVDTPLSTTGGVVGLEGNLAPEGAIVKIAGMSDDQLVFTGPAR 415

Query: 414 VFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAE-------VGNMGLPPKVLKK 466
           VFE  +D    +   N    E  + V++N GP G PGM E       +   G+  KV   
Sbjct: 416 VFECEEDAFEAV--QNRAYAEGDVFVIRNEGPAGGPGMREMLATTAALSGQGMGKKV--- 470

Query: 467 GILDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526
                  I+D R SG   G  V H  PEAA GGP+A++K+GDMI +D     L + +S++
Sbjct: 471 -----ALITDGRFSGATRGFCVGHVGPEAAHGGPIAMLKDGDMITIDALKGELSVALSED 525

Query: 527 ELARRLAEWQ-PNHDLPTSGYAFLHQQHVEGADTGA 561
           ELA R   W  P   +  SG  + + Q V GA  GA
Sbjct: 526 ELAARKDAWSGPRETIYASGALWKYAQLVGGARLGA 561


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: 906
Number of extensions: 58
Number of successful extensions: 7
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