GapMind for catabolism of small carbon sources

 

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

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 WP_085634854.1 MGEO_RS01140 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>NCBI__GCF_002115805.1:WP_085634854.1
          Length = 587

 Score =  297 bits (761), Expect = 7e-85
 Identities = 187/534 (35%), Positives = 283/534 (52%), Gaps = 51/534 (9%)

Query: 44  RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRN 103
           +P++G+   W++  PCN  L   A+ VK GV +A G P E    + ++        M  +
Sbjct: 41  QPLVGVATCWNEAAPCNIALNRQAQAVKMGVKQAFGTPREFTTITVTDGIAMGHEGMRSS 100

Query: 104 LA-----ALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158
           LA     A  VE  +RG   D  V L GCDK+ P ++M     ++PS+ + GG +L G  
Sbjct: 101 LASREAIADTVELTMRGHCYDAVVGLAGCDKSLPGMMMAMVRLNVPSVFIYGGSILPG-- 158

Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEA-----------------EASMSRSSGTCN 201
                     + +  E  +  ++T  +  EA                 E     S+G C 
Sbjct: 159 ------KAPQVAEIPEDFRTRDLTVQDMFEAVGRHQNNELSDKALDMLERVACPSAGACG 212

Query: 202 TMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQ 261
              TA+TMA ++EA+G+AL  ++ +P     R    + +GR ++ +++ ++K  +I+T++
Sbjct: 213 GQFTANTMACVSEAIGLALFNSSGMPAPYESRDAYGEASGRAVMDLIEQNIKARDIVTRE 272

Query: 262 AFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLME 321
           A ENA R  A  GGSTNA +HL AIA   GI+  L+D     +D P  V+L P G Y+ +
Sbjct: 273 ALENAARVVACTGGSTNAGLHLPAIAHEAGIEFYLEDVCDIFKDTPYFVDLKPGGTYVAK 332

Query: 322 EFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED--VILPAEKALTSS 379
           + + AGG+PVV+K L +AGL+H+D +T S  T+ +E+ D +    D  VI   E  +T +
Sbjct: 333 DLYDAGGIPVVMKELRKAGLIHEDCVTASTRTIGEEL-DRIEREADGKVIYSIETPITKT 391

Query: 380 GGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMV 439
           GG+V L+GNLAP+GA++K +       +  G A VFE  +D  A +     D  E  ++V
Sbjct: 392 GGVVGLKGNLAPEGAIVKVAGIKAEDQIFTGPARVFECEEDAFAAVK--ARDYKEGEVIV 449

Query: 440 MKNCGPKGYPGMAE-------VGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHTS 492
           ++N GP G PGM E       +   G+  KV          I+D R SG   G  V H  
Sbjct: 450 IRNEGPAGGPGMREMLATTAALSGQGMGKKV--------ALITDGRFSGATRGFCVGHVG 501

Query: 493 PEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQ-PNHDLPTSG 545
           PEAA+GGP+A++KNGDMI +D  N  L +D+SDEELA+R A+W  P   + TSG
Sbjct: 502 PEAALGGPIALLKNGDMITIDAVNGSLSVDLSDEELAQRKADWTGPRETIYTSG 555


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: 903
Number of extensions: 54
Number of successful extensions: 6
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: 587
Length adjustment: 36
Effective length of query: 543
Effective length of database: 551
Effective search space:   299193
Effective search space used:   299193
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 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