GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Sphingomonas koreensis DSMZ 15582

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ga0059261_2649 Ga0059261_2649 Dihydroxyacid dehydratase/phosphogluconate dehydratase

Query= reanno::BFirm:BPHYT_RS19730
         (577 letters)



>FitnessBrowser__Korea:Ga0059261_2649
          Length = 618

 Score =  465 bits (1197), Expect = e-135
 Identities = 258/539 (47%), Positives = 348/539 (64%), Gaps = 16/539 (2%)

Query: 8   KKPLRSQAWFGLKDRDGF--LHRSWMKNQGIPHDEF-DGRPVIGICNTWSELTPCNAHFR 64
           ++ LRS AWF   D      L+     N G+   E   GRP+IGI  T S+L+PCN H  
Sbjct: 26  ERKLRSAAWFDNPDNIDMTALYLERYLNFGLSLKELRSGRPIIGIAQTGSDLSPCNRHHL 85

Query: 65  ELAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILL 124
            LAE V++G+ +AGG+ +EFPV  + ET  RPTA L RNLA + + E++ G P+DGV+L 
Sbjct: 86  VLAERVREGIRDAGGIAIEFPVHPIQETGKRPTAGLDRNLAYLGLVEALYGYPLDGVVLT 145

Query: 125 VGCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQE 184
           +GCDKTTPA LM AA+ N+PA+A+S GPMLNG  +G+  GSGT VW+  + + AG +  +
Sbjct: 146 IGCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGERTGSGTIVWKARQMLAAGEIDDD 205

Query: 185 EFTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRI 244
           EF    +    S G+C TMGTA+TM S+ E+LGM LP +AAIPA    RQ +A+  G R 
Sbjct: 206 EFIRLVASSAPSTGYCNTMGTATTMNSLAEALGMSLPGSAAIPAPHRDRQEVAYQTGLRA 265

Query: 245 VDMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGS 303
           V++VR D+    ILTR+AFENAI  N+AIGGSTNA +HL A+A+ IGV+L ++ W E G 
Sbjct: 266 VELVRADVKPSDILTREAFENAIVVNSAIGGSTNAPIHLAAIARHIGVDLPIDAWQEKGH 325

Query: 304 NVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANY 363
            VP LVNLQP+GEYL ED+Y AGG+PAV+ QL + GL+H++A TVNGK++  N R  A  
Sbjct: 326 AVPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLIDAGLIHEDAGTVNGKSIGANCRGVAIE 385

Query: 364 DEKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKH-----------RGRAV 412
           DEKVI  FA+P K  AG  VL+GNL    A++K S  +                  G AV
Sbjct: 386 DEKVIRPFAQPLKDAAGFIVLRGNLF-ESAIMKTSVISDEFRDRYLSNPDDPDAFEGPAV 444

Query: 413 VFENIEELHAKIDDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVR 472
           VF+  E+ HA+IDD +L I    ++ ++GAGP GYPG AEV NM  P  ++++GI  +  
Sbjct: 445 VFDGPEDYHARIDDPALGITPETLLFMRGAGPVGYPGAAEVVNMRPPAYLIREGIHALPC 504

Query: 473 ISDGRMSGTAYGAVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRR 531
           I DGR SGT+    +L+ SPEAAA G LA ++TGD + +D+ +    + +   ELA RR
Sbjct: 505 IGDGRQSGTSGSPSILNASPEAAAMGGLALIRTGDRVRIDLGKGTADVLIPSAELAERR 563


Lambda     K      H
   0.318    0.135    0.401 

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: 993
Number of extensions: 59
Number of successful extensions: 3
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: 577
Length of database: 618
Length adjustment: 37
Effective length of query: 540
Effective length of database: 581
Effective search space:   313740
Effective search space used:   313740
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