GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kdgK in Pseudomonas fluorescens FW300-N1B4

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)

Query= SwissProt::P50845
         (324 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765 2-ketogluconate
           kinase (EC 2.7.1.13)
          Length = 339

 Score =  311 bits (797), Expect = 1e-89
 Identities = 164/314 (52%), Positives = 215/314 (68%), Gaps = 4/314 (1%)

Query: 2   KLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQ 61
           ++D ++FGE+MAMF A + G L +V  F K +AGA+SNVA GL+RLGF + W+S+VG D 
Sbjct: 3   EIDILSFGETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGADS 62

Query: 62  LGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAE 120
           LG F++  L+K+G+D S V      +PTG  LKS+  +G DP V Y+R+ SAAS L+   
Sbjct: 63  LGRFVIDTLEKQGLDCSHV-DIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQS 121

Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180
                 + A HLH TGIPPALSA  ++ ++ +M  MRNAG+++SFDPN+RPSLW  +  M
Sbjct: 122 IAPQLLE-ARHLHATGIPPALSAAAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQM 180

Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240
           +  IN LA LA W  PG++EG LLTG + P  IA +YL +GA  VAIKLG  GAY++T  
Sbjct: 181 IREINRLAALAHWVLPGLSEGRLLTGFEDPADIAAFYLDQGAEAVAIKLGPAGAYYRTHL 240

Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300
            EGF+ G  V+ VVDTVGAGDGFAVG+IS +L+  S   AVQR N IG+  VQ+ GDM+G
Sbjct: 241 DEGFVAGVPVETVVDTVGAGDGFAVGLISALLENHSVAQAVQRANWIGSRAVQSRGDMEG 300

Query: 301 LPTR-EKLASFLSA 313
           LPTR E  A F  A
Sbjct: 301 LPTRLEMFAEFEGA 314


Lambda     K      H
   0.317    0.135    0.399 

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: 348
Number of extensions: 19
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: 324
Length of database: 339
Length adjustment: 28
Effective length of query: 296
Effective length of database: 311
Effective search space:    92056
Effective search space used:    92056
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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