GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_2649 Ga0059261_2649
           Dihydroxyacid dehydratase/phosphogluconate dehydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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