GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Cola:Echvi_2055
          Length = 561

 Score =  300 bits (769), Expect = 8e-86
 Identities = 178/510 (34%), Positives = 284/510 (55%), Gaps = 23/510 (4%)

Query: 44  RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEA--GGFPLEVPVFSASENTFRPTAMMY 101
           +P +G+ +   +  PCN HL   AE +KA   +A   GF       S  ++    + M Y
Sbjct: 37  QPFVGVASCGYESNPCNMHLNSFAEDIKASTNQADLSGFIFNTIGISDGQS-MGTSGMRY 95

Query: 102 ----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGY 157
               R + A ++E  I G   DG V + GCDK  P ++MG    + P I+V GG + +G 
Sbjct: 96  SLPSREVIADSIESFILGHSFDGVVTIPGCDKNMPGVVMGMLRVNRPGIMVFGGTIRSGN 155

Query: 158 FRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALG 217
           ++GE++   +    + + +  G+++  +++    +    +G C  M TA+TM+S  EA+G
Sbjct: 156 YKGEKLNIVSAFEAYGKKIN-GQISDEDYMGVIKNACPGAGACGGMYTANTMSSAIEAMG 214

Query: 218 MALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGST 277
           ++L  +++ P     ++   +  G+ I Q++  D+KP +I+TK++ ENA+R   A+GGST
Sbjct: 215 LSLPFSSSYPATSKEKREECKNIGKYIKQLLALDIKPKDIITKKSLENAVRVTVALGGST 274

Query: 278 NAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLG 337
           NA +H+LAIA   GID +L+D+ R   + P + +  PSGK++ME+ +  GGLP  LK   
Sbjct: 275 NAALHILAIARTAGIDFTLEDFKRINAETPVLGDFKPSGKFMMEDLYEMGGLPAFLKYFL 334

Query: 338 EAGLLHKDALTVSGETVWDEVKD---VVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGA 394
             GLLH D LTV+G+T+ + ++D   V    E VI P +  +  SG + VL GNLAP+GA
Sbjct: 335 NEGLLHGDCLTVTGKTMAENLEDIDPVKPSKESVIHPLDNPIKPSGHLCVLHGNLAPEGA 394

Query: 395 VLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEV 454
           V K S          G A VF+D     A +   N +I +  ++V++  GPKG PGM E+
Sbjct: 395 VAKISGKEGKSFT--GTAKVFDDEPSANAAMK--NKEIQKGDVVVIRYVGPKGGPGMPEM 450

Query: 455 GNMGLPPKVLKKGI---LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIE 511
               L P  +  G     D+  I+D R SG  +G VV H +PEA +GGP+ ++K+GD+I 
Sbjct: 451 ----LKPTSIIIGAGLGSDVALITDGRFSGGTHGFVVGHVTPEAYLGGPIGLLKDGDVIT 506

Query: 512 LDVPNRRLHLDISDEELARRLAEWQPNHDL 541
           +D  +  + +D+S+ E A R   W+ N DL
Sbjct: 507 IDAESLEIRVDVSEAEFAERKKNWK-NKDL 535


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: 865
Number of extensions: 50
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 561
Length adjustment: 36
Effective length of query: 543
Effective length of database: 525
Effective search space:   285075
Effective search space used:   285075
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