GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Bacteroides thetaiotaomicron VPI-5482

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate 350016 BT0488 2-dehydro-3-deoxygluconokinase (NCBI ptt file)

Query= BRENDA::Q9WXS2
         (339 letters)



>FitnessBrowser__Btheta:350016
          Length = 341

 Score =  361 bits (927), Expect = e-104
 Identities = 185/339 (54%), Positives = 238/339 (70%), Gaps = 2/339 (0%)

Query: 2   KVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLG 61
           KVVT GEIMLRLS P + R  Q+DSFDV YGG EANVA   A  G +AYFVTKLP + +G
Sbjct: 4   KVVTLGEIMLRLSTPGNTRFVQSDSFDVVYGGGEANVAVSCANYGHEAYFVTKLPKHEIG 63

Query: 62  DAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121
            +A   LRK+GVKTD+IARGG+R+GIY+LE GAS RPSKV+YDRAHSAI+EA   DFD++
Sbjct: 64  QSAVNALRKYGVKTDFIARGGDRVGIYYLETGASMRPSKVIYDRAHSAIAEADAADFDFD 123

Query: 122 KILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVM 181
            I++GA WFH+SGITP +  +   +   A + A   GVTVS DLN+R +LWTKE+AQ +M
Sbjct: 124 AIMEGADWFHWSGITPAISDKAAELTRLACEAAKRHGVTVSVDLNFRKKLWTKEKAQSIM 183

Query: 182 IPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITL 241
            P M+YVDV I NEED E  LG   +  D++ G  + E Y  I +++ +++ FK V  TL
Sbjct: 184 KPLMKYVDVCIGNEEDAELCLGFKPDA-DVEAGHTDAEGYKGIFQQMMKEFGFKYVVSTL 242

Query: 242 RESISATVNYWSVMVFENGQPHFSNRYEIH-IVDRVGAGDSFAGALIYGSLMGFDSQKKA 300
           RES SAT N W  M++   + + S RY+I  I+DRVG GDSF+G +I+G +   +     
Sbjct: 243 RESFSATHNGWKAMIYNGEEFYTSKRYDIDPIIDRVGGGDSFSGGIIHGLMTKPNQGAAL 302

Query: 301 EFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRVER 339
           EFA AAS LKHTI GDF ++S+EE+E LA G  SGRV+R
Sbjct: 303 EFAVAASALKHTINGDFNLVSVEEVEALAGGDASGRVQR 341


Lambda     K      H
   0.319    0.136    0.397 

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: 359
Number of extensions: 12
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: 339
Length of database: 341
Length adjustment: 28
Effective length of query: 311
Effective length of database: 313
Effective search space:    97343
Effective search space used:    97343
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 (21.8 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