GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Synechococcus elongatus PCC 7942

Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Synpcc7942_0459 Synpcc7942_0459 glutathione-dependent formaldehyde dehydrogenase

Query= BRENDA::Q97YM2
         (349 letters)



>FitnessBrowser__SynE:Synpcc7942_0459
          Length = 369

 Score =  118 bits (296), Expect = 2e-31
 Identities = 116/380 (30%), Positives = 180/380 (47%), Gaps = 50/380 (13%)

Query: 7   VKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPI 66
           +KS+AA+     +PL+IE+V++  PQ  EV++++   GVC TD     G + +  F  P 
Sbjct: 1   MKSRAAIAWAAGQPLTIEEVDVQAPQAGEVMVKLVATGVCHTDAFTLSGADPEGIF--PC 58

Query: 67  ILGHENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICK-------NQII 118
           ILGHE AG +VEVGE +  V  GD+V+   T     C++C+ GK N+C+         ++
Sbjct: 59  ILGHEGAGIVVEVGEGVTSVAVGDHVIPLYTPECGECKFCKSGKTNLCQAIRATQGKGLM 118

Query: 119 PGQTT----NG----------GFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTSMGA 163
           P  T+    NG           FSEY ++     + K+N  + ++   L   G TT +GA
Sbjct: 119 PDGTSRFSLNGQPIYHFMGTSTFSEYTVLPEIA-IAKINPAAALDKVCLLGCGITTGIGA 177

Query: 164 IRQALPFISKFAEP--VVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALELG 221
           +           EP   V V G+GG+ +  IQ    L K   I+ I  +    +FA +LG
Sbjct: 178 VLNTAK-----VEPGSTVAVFGLGGVGLSVIQ-GAVLAKASRILAIDINPDKAEFAKQLG 231

Query: 222 ADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIILVG 274
           A      KD     + +I +LTDG G   + + +G   T     +   +   E  II V 
Sbjct: 232 ATDFINPKDYDRPIQEVIVELTDG-GVDYSFEAIGNVNTMRAALESCHKGWGESTIIGVA 290

Query: 275 MEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVRLSESGKIK--PYIIKV-PLDD 328
             G+ +S   F      VW     G   G  + L   V    +G+IK   ++ +  PL++
Sbjct: 291 GAGQEISTRPFQLVTGRVWRGSAFGGVKGR-SQLPGYVEQYLNGQIKVDEFVTETRPLEE 349

Query: 329 INKAFTNLDEGRVDGRQVIT 348
           IN+AF ++  G+V  R VIT
Sbjct: 350 INEAFEDMHAGKVI-RTVIT 368


Lambda     K      H
   0.317    0.136    0.389 

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: 322
Number of extensions: 23
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: 349
Length of database: 369
Length adjustment: 29
Effective length of query: 320
Effective length of database: 340
Effective search space:   108800
Effective search space used:   108800
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 (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