GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas simiae WCS417

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 GFF2464 PS417_12565 2-dehydro-3-deoxygluconokinase

Query= SwissProt::P50845
         (324 letters)



>FitnessBrowser__WCS417:GFF2464
          Length = 313

 Score =  327 bits (837), Expect = 3e-94
 Identities = 167/307 (54%), Positives = 219/307 (71%), Gaps = 3/307 (0%)

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

Query: 62  LGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEGD-PQVTYYRKNSAASTLTTAE 120
           LG F++  L +EG+D  R +     +PTG  LKS+ + GD PQV Y+RK SAAS L+ A 
Sbjct: 63  LGRFVVDTLTQEGLDC-RHVAVDPAHPTGFQLKSREETGDDPQVEYFRKGSAASHLSIAA 121

Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180
                 Q A HLH TGIPPALS   ++ +  +M  MR AG+++SFDPN+RPSLW +Q TM
Sbjct: 122 ISPALLQ-ARHLHATGIPPALSEATRELSVELMTQMRKAGRSVSFDPNLRPSLWANQQTM 180

Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240
           +  IN LAGLADW  PG+ EG  LTG   P  IA +YL +GA  VAIKLG +GAY++T  
Sbjct: 181 IREINALAGLADWVLPGLGEGRQLTGFDDPADIAAFYLDQGAEAVAIKLGPDGAYYRTHL 240

Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300
            +GF+   RVD+VVDTVGAGDGFAVG+IS +L+ LS+ +AVQRGN IG+  VQ+ GDM+G
Sbjct: 241 DQGFVAAVRVDKVVDTVGAGDGFAVGMISALLENLSFPEAVQRGNWIGSRAVQSRGDMEG 300

Query: 301 LPTREKL 307
           LP R +L
Sbjct: 301 LPARSEL 307


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: 346
Number of extensions: 17
Number of successful extensions: 4
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: 313
Length adjustment: 27
Effective length of query: 297
Effective length of database: 286
Effective search space:    84942
Effective search space used:    84942
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