GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Dyella japonica UNC79MFTsu3.2

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate N515DRAFT_2221 N515DRAFT_2221 2-dehydro-3-deoxygluconokinase

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2221
          Length = 311

 Score =  108 bits (270), Expect = 2e-28
 Identities = 88/275 (32%), Positives = 130/275 (47%), Gaps = 22/275 (8%)

Query: 41  GGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMI 100
           GG  +N  +AAAR  A V +I+  GDD FG  +R+ ++ +G+  + V+  P  PTG+  +
Sbjct: 31  GGDTSNFCIAAARQGASVDYISATGDDRFGQGLRDLWQAEGVGHSHVRTDPQAPTGVYFV 90

Query: 101 QVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYL------LMQLETPLDGILKAAQ 154
               SG +   + A + A     A  P   AI  AR L      L   +   D  L+A  
Sbjct: 91  SHDASGHHFDYLRAGSAASRYVPAYLPG-QAIASARALHLSGISLAISQDACDAGLEAMA 149

Query: 155 EAKTA------KTNVILNPAP---ARELPDELLKCVDLITPNETEAEVLTGITVYDDSSA 205
           +A+ A       TN+ L   P   AR +  E L+  DL  P+  +        V D    
Sbjct: 150 QARAAGVMVSFDTNLRLRLWPLARARAVMREALRLCDLCLPSWDDITA-----VLDCHEP 204

Query: 206 QQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGL 265
               D L   GIE+V + +G++G +++       +P   V A D T AGD F GA V  L
Sbjct: 205 DAILDTLLDCGIELVALKMGARGCYVATPESRILVPPHAVDAVDATGAGDCFGGAFVARL 264

Query: 266 LQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAE 300
           +      +A ++A+ AAA+S T +GA  SIP RAE
Sbjct: 265 VAGDDAVAAARYANVAAALSTTGYGAIASIP-RAE 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: 173
Number of extensions: 4
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: 309
Length of database: 311
Length adjustment: 27
Effective length of query: 282
Effective length of database: 284
Effective search space:    80088
Effective search space used:    80088
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