GapMind for catabolism of small carbon sources

 

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

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate N515DRAFT_2221 N515DRAFT_2221 2-dehydro-3-deoxygluconokinase

Query= reanno::Cup4G11:RR42_RS28860
         (311 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2221
          Length = 311

 Score =  386 bits (992), Expect = e-112
 Identities = 199/296 (67%), Positives = 220/296 (74%)

Query: 4   DILAFGEALVEFNQQPDDPSRYLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLL 63
           +IL+FGE L EFNQ     + +  G+GGDTSNFCIAAARQGA   YISA G+D FG+ L 
Sbjct: 5   EILSFGEPLAEFNQTQAGSAAWRLGYGGDTSNFCIAAARQGASVDYISATGDDRFGQGLR 64

Query: 64  ALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHRFDYLRSGSAASHYSHENLPHHAIAEA 123
            LW  E V   HVR D  APTGVYFV+HDA GH FDYLR+GSAAS Y    LP  AIA A
Sbjct: 65  DLWQAEGVGHSHVRTDPQAPTGVYFVSHDASGHHFDYLRAGSAASRYVPAYLPGQAIASA 124

Query: 124 RYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFAL 183
           R LH+SGISLAIS  ACDAGL AM  AR AG  V+ DTNLRLRLW LARAR +MREA  L
Sbjct: 125 RALHLSGISLAISQDACDAGLEAMAQARAAGVMVSFDTNLRLRLWPLARARAVMREALRL 184

Query: 184 TDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV 243
            D+CLPSWDDIT +    + DAI+D LL CGI LVALK+G  G YVATPE+R LVPP+ V
Sbjct: 185 CDLCLPSWDDITAVLDCHEPDAILDTLLDCGIELVALKMGARGCYVATPESRILVPPHAV 244

Query: 244 RPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPSIETV 299
             VDATGAGDCFGG+FVARL AGDD   AARYANVAAALSTTGYGA+A IP  E V
Sbjct: 245 DAVDATGAGDCFGGAFVARLVAGDDAVAAARYANVAAALSTTGYGAIASIPRAEAV 300


Lambda     K      H
   0.321    0.136    0.409 

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: 378
Number of extensions: 15
Number of successful extensions: 1
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: 311
Length of database: 311
Length adjustment: 27
Effective length of query: 284
Effective length of database: 284
Effective search space:    80656
Effective search space used:    80656
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 (21.9 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