GapMind for catabolism of small carbon sources

 

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

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate N515DRAFT_2221 N515DRAFT_2221 2-dehydro-3-deoxygluconokinase

Query= BRENDA::O04897
         (347 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2221
          Length = 311

 Score =  132 bits (332), Expect = 1e-35
 Identities = 104/313 (33%), Positives = 152/313 (48%), Gaps = 20/313 (6%)

Query: 28  VVCFGEMLIDFIPTVAGVSLAEAPAFEKAPGGAPANVAVCISKLGGSSAFIGKVGDDEFG 87
           ++ FGE L +F  T AG     + A+    GG  +N  +  ++ G S  +I   GDD FG
Sbjct: 6   ILSFGEPLAEFNQTQAG-----SAAWRLGYGGDTSNFCIAAARQGASVDYISATGDDRFG 60

Query: 88  RMLADILKQNNVDNSGMRFDHDARTALAFITLTAEGEREFVFFRNPSADMLLRESELDVD 147
           + L D+ +   V +S +R D  A T + F++  A G   F + R  SA      + L   
Sbjct: 61  QGLRDLWQAEGVGHSHVRTDPQAPTGVYFVSHDASG-HHFDYLRAGSAASRYVPAYLPGQ 119

Query: 148 LIKKATIFHYGSISL-IDEPCRSTHLAAMDIAKRSGSILSYDPNLRLPLWPSEDAARSGI 206
            I  A   H   ISL I +      L AM  A+ +G ++S+D NLRL LWP    AR+ +
Sbjct: 120 AIASARALHLSGISLAISQDACDAGLEAMAQARAAGVMVSFDTNLRLRLWPLA-RARAVM 178

Query: 207 MSVWNLADIIKISEDEISFLTGADDPNDDEVVLKRLFHPNLKLLLVTEGSAGCRYYTKEF 266
                L D+   S D+I   T   D ++ + +L  L    ++L+ +  G+ GC   T E 
Sbjct: 179 REALRLCDLCLPSWDDI---TAVLDCHEPDAILDTLLDCGIELVALKMGARGCYVATPES 235

Query: 267 KGRVNSIKVKAVDTTGAGDAFTGG-VLKCLASDASLYQDEKRLREAIFFANVCAALTVTG 325
           +  V    V AVD TGAGD F G  V + +A D ++         A  +ANV AAL+ TG
Sbjct: 236 RILVPPHAVDAVDATGAGDCFGGAFVARLVAGDDAV--------AAARYANVAAALSTTG 287

Query: 326 RGGIPSLPTQDAV 338
            G I S+P  +AV
Sbjct: 288 YGAIASIPRAEAV 300


Lambda     K      H
   0.319    0.135    0.389 

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: 239
Number of extensions: 13
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: 347
Length of database: 311
Length adjustment: 28
Effective length of query: 319
Effective length of database: 283
Effective search space:    90277
Effective search space used:    90277
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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