GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Korea:Ga0059261_2649
          Length = 618

 Score =  447 bits (1149), Expect = e-130
 Identities = 243/537 (45%), Positives = 341/537 (63%), Gaps = 15/537 (2%)

Query: 9   RKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65
           RKLRS  W+          +Y   +L       +L  GRP+IGI  T SD++PCN H   
Sbjct: 27  RKLRSAAWFDNPDNIDMTALYLERYLNFGLSLKELRSGRPIIGIAQTGSDLSPCNRHHLV 86

Query: 66  LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125
           LAE+V+ G+ +AGG  +E PV    E   RPTA + RNLA L + EA+ G P+DG VL +
Sbjct: 87  LAERVREGIRDAGGIAIEFPVHPIQETGKRPTAGLDRNLAYLGLVEALYGYPLDGVVLTI 146

Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185
           GCDKTTP+ LM AA+ ++P+I ++ GPMLNG+ +GER GSGT +WK  +M+ AGE+   E
Sbjct: 147 GCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGERTGSGTIVWKARQMLAAGEIDDDE 206

Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245
           F+   AS + S+G CNTMGTA+TM S+AEALGM+L G+AAIP     R+ +A  TG R V
Sbjct: 207 FIRLVASSAPSTGYCNTMGTATTMNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGLRAV 266

Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305
           ++V+ D+KPS+I+T++AFENAI  N+AIGGSTNA IHL AIA  +G+DL +D W   G  
Sbjct: 267 ELVRADVKPSDILTREAFENAIVVNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEKGHA 326

Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365
           VP +VNL P+G+YL E+++ AGG+P V+ +L +AGL+H+DA TV+G+++    + V   +
Sbjct: 327 VPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVAIED 386

Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAVV 414
           E VI P  + L  + G +VLRGNL  + A++K S  S                 +G AVV
Sbjct: 387 EKVIRPFAQPLKDAAGFIVLRGNLF-ESAIMKTSVISDEFRDRYLSNPDDPDAFEGPAVV 445

Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474
           F+  +DY A+I+D  L I    ++ M+  GP GYPG AEV NM  P  ++++GI  +  I
Sbjct: 446 FDGPEDYHARIDDPALGITPETLLFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALPCI 505

Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531
            D R SGT+    +L+ SPEAA  G LA+++ GD + +D+      + I   ELA R
Sbjct: 506 GDGRQSGTSGSPSILNASPEAAAMGGLALIRTGDRVRIDLGKGTADVLIPSAELAER 562


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: 1046
Number of extensions: 56
Number of successful extensions: 2
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: 618
Length adjustment: 37
Effective length of query: 542
Effective length of database: 581
Effective search space:   314902
Effective search space used:   314902
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