GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Pseudomonas fluorescens FW300-N2C3

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 AO356_00445 AO356_00445 ketodeoxygluconokinase

Query= SwissProt::P45416
         (310 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00445
          Length = 306

 Score =  285 bits (729), Expect = 1e-81
 Identities = 155/300 (51%), Positives = 196/300 (65%), Gaps = 5/300 (1%)

Query: 6   IAIIGECMIELSQKG-ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFSSEM 64
           IA+IGECMIEL Q+    L + FGGDTLNTAVY+SR +      V YVTALG DSFS  M
Sbjct: 10  IALIGECMIELQQRADGSLLQSFGGDTLNTAVYLSRALGNRGA-VDYVTALGDDSFSDAM 68

Query: 65  MASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADTISQ 124
              W +E +    +QRL  +LPGLY I+TDA GER F YWRN+AA R    +P A  I  
Sbjct: 69  CECWAEENIGLQRVQRLPGRLPGLYCIQTDAAGERRFLYWRNEAAVRECFTTPAAAPILA 128

Query: 125 QLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEETRQA 184
            L  +D +Y SG++LA+L +  RARL+  L   R  G +V+FDNNYRPRLW S E  R A
Sbjct: 129 ALPDYDVLYFSGVTLAVLGEQGRARLIETLVEARRRGAQVVFDNNYRPRLWASIEAARAA 188

Query: 185 YSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQGEAL 244
           Y  +L   ++A LT++DE  L+G    D V       G  EVV+KRGA+ACL+   GE+ 
Sbjct: 189 YRSVLPYVELALLTVEDEQALFGYADTDAVFAAYGQLGTPEVVLKRGAEACLIRCDGES- 247

Query: 245 LEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGAIIP 304
            E+PA ++  E+VVDTTAAGDSFSA YL+ RL GG+  +AA+ GHL AS VIQ  GA++P
Sbjct: 248 YEIPAQRV--ERVVDTTAAGDSFSAAYLASRLLGGTPAEAAESGHLLASRVIQVPGALMP 305


Lambda     K      H
   0.318    0.134    0.390 

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: 295
Number of extensions: 16
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: 310
Length of database: 306
Length adjustment: 27
Effective length of query: 283
Effective length of database: 279
Effective search space:    78957
Effective search space used:    78957
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 (21.7 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