GapMind for catabolism of small carbon sources

 

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

Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate AO356_26150 AO356_26150 2-dehydro-3-deoxyglucarate aldolase

Query= SwissProt::Q47098
         (262 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26150
          Length = 266

 Score =  276 bits (706), Expect = 3e-79
 Identities = 136/257 (52%), Positives = 184/257 (71%)

Query: 3   NSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIAP 62
           N+FKAAL +   Q G+W G +S Y+AE++AG G+DW+LIDGEHAPN V +VL+QLQA+AP
Sbjct: 6   NAFKAALTSKHTQYGIWAGFASGYAAEIVAGTGYDWMLIDGEHAPNTVPSVLSQLQAVAP 65

Query: 63  YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSAL 122
           Y + PVVR    D   IKQLLDVG QTL++PMV+ A++A+  VRA RYPP G+RGVG  L
Sbjct: 66  YATAPVVRAVTGDANLIKQLLDVGAQTLMIPMVETAEQAQALVRAMRYPPHGMRGVGGGL 125

Query: 123 ARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMGY 182
            RA+RW+ + +YL  A++++C++VQ+E+R  ++N+  I  VEGVD VFIGPADLS  +G+
Sbjct: 126 TRATRWDGVANYLTTAHEELCLIVQVESRTGVENVEAIAAVEGVDAVFIGPADLSIGLGH 185

Query: 183 AGNPQHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVDTTLLARA 242
           AGNP HPEVQ  I+ A+     +GKA GIL  N + A+RY   G  F+AV +D +LL ++
Sbjct: 186 AGNPGHPEVQERIQFAVNATLAAGKACGILAPNAEDARRYQGWGCQFIAVAIDISLLRQS 245

Query: 243 AEALAARFGAQATAVKP 259
           A A  A +   ATA  P
Sbjct: 246 ALATLALYREPATAQTP 262


Lambda     K      H
   0.317    0.133    0.387 

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: 208
Number of extensions: 7
Number of successful extensions: 1
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: 262
Length of database: 266
Length adjustment: 25
Effective length of query: 237
Effective length of database: 241
Effective search space:    57117
Effective search space used:    57117
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: 47 (22.7 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