GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Sphingomonas koreensis DSMZ 15582

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate Ga0059261_0568 Ga0059261_0568 Sugar kinases, ribokinase family

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__Korea:Ga0059261_0568
          Length = 315

 Score =  209 bits (531), Expect = 9e-59
 Identities = 130/303 (42%), Positives = 176/303 (58%), Gaps = 14/303 (4%)

Query: 6   KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQ-ADVGFIACV 64
           +++V GS N D V++ P  P PGET+ G +  V+PGGKGANQAVAAAR   AD   +  +
Sbjct: 9   RVLVAGSANVDFVVRAPHIPAPGETVLGGDLSVVPGGKGANQAVAAARAGGADTAMLLAL 68

Query: 65  GDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAA 124
           GDD     + +S +  G++   V+     PTG A+I VSD  EN+I ++  AN +L    
Sbjct: 69  GDDPSAGVLEDSLRAAGVSLHVVRASR--PTGAALITVSDGAENAITVAQGANGELAPE- 125

Query: 125 IEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLI 184
               L ++    +LL+QLETP+  ++  A+ A+ A   V+LN APA+ LP ELL  VDL+
Sbjct: 126 ---HLPSLEGVSWLLLQLETPIASVIAYARAARVAGVGVMLNAAPAQPLPAELLALVDLL 182

Query: 185 TPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFV 244
             NE E   +TG      S A++ A      G+   ++TLG +G   + +G       F 
Sbjct: 183 VVNEEELAAITG---KQGSIAERVART----GVATTVVTLGERGCCAADHGTLISQAAFS 235

Query: 245 VKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAF 304
           V ATDTTAAGDTF G L   L     L  A++ A AAAA+S TR GAQTSIPT AEV AF
Sbjct: 236 VAATDTTAAGDTFCGVLGAALAGGTDLLGALRRAAAAAALSATRAGAQTSIPTAAEVAAF 295

Query: 305 LAE 307
           LA+
Sbjct: 296 LAD 298


Lambda     K      H
   0.316    0.132    0.373 

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: 237
Number of extensions: 10
Number of successful extensions: 4
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: 309
Length of database: 315
Length adjustment: 27
Effective length of query: 282
Effective length of database: 288
Effective search space:    81216
Effective search space used:    81216
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 (21.6 bits)
S2: 48 (23.1 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