GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguK in Burkholderia phytofirmans PsJN

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate BPHYT_RS11300 BPHYT_RS11300 2-dehydro-3-deoxygluconokinase

Query= metacyc::MONOMER-12748
         (320 letters)



>FitnessBrowser__BFirm:BPHYT_RS11300
          Length = 327

 Score =  373 bits (957), Expect = e-108
 Identities = 187/305 (61%), Positives = 230/305 (75%), Gaps = 1/305 (0%)

Query: 4   IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63
           +D++++GE MAMFVA   G LA V  F KR+AGAD NVAIGL+RLGFKV W+SRVGNDS 
Sbjct: 8   LDVITYGEAMAMFVAAETGPLAGVGQFTKRVAGADLNVAIGLSRLGFKVGWMSRVGNDSF 67

Query: 64  GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123
           G++V DTL  EG+D   V  D  +PTGFQLKS+ D G DP +EYFR+GSAASHL+++D  
Sbjct: 68  GQYVRDTLTKEGIDQGCVTTDERYPTGFQLKSKNDDGSDPAIEYFRKGSAASHLSLADYA 127

Query: 124 PA-LLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182
              +L+ARHLH TG+ PA+S S+REL+ HL    R+AG ++SFDPNLRP LWPS A M+ 
Sbjct: 128 ADYVLQARHLHLTGVAPAISASSRELAFHLAREMRAAGKTISFDPNLRPTLWPSRAAMVE 187

Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQLDA 242
            +N LAALA WVLPG+ EG +LTG   P DIA FYL+QGA  V+IKLGA GAY+RT  DA
Sbjct: 188 GLNALAALADWVLPGIGEGEILTGYTQPDDIAKFYLEQGARGVIIKLGAQGAYFRTADDA 247

Query: 243 GFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGLP 302
             + G PVA+VVDTVGAGDGFAVG++SALLE + + +AV R N IG+ A+Q  GD EGLP
Sbjct: 248 AMIAGQPVAKVVDTVGAGDGFAVGVVSALLEGKSLPQAVARGNRIGALAIQVIGDSEGLP 307

Query: 303 LRHEL 307
            R EL
Sbjct: 308 SRAEL 312


Lambda     K      H
   0.321    0.138    0.414 

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: 385
Number of extensions: 18
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: 320
Length of database: 327
Length adjustment: 28
Effective length of query: 292
Effective length of database: 299
Effective search space:    87308
Effective search space used:    87308
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