GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Synechococcus elongatus PCC 7942

Align xylitol 2-dehydrogenase (EC 1.1.1.9) (characterized)
to candidate Synpcc7942_0459 Synpcc7942_0459 glutathione-dependent formaldehyde dehydrogenase

Query= reanno::WCS417:GFF3461
         (359 letters)



>FitnessBrowser__SynE:Synpcc7942_0459
          Length = 369

 Score =  106 bits (264), Expect = 1e-27
 Identities = 100/366 (27%), Positives = 159/366 (43%), Gaps = 45/366 (12%)

Query: 20  LERIGKPQARANELVIRIAACGICASDCKCHSGAAMFWGGDNPWVKAPVVPGHEFFGYVV 79
           +E +     +A E+++++ A G+C +D    SGA       +P    P + GHE  G VV
Sbjct: 17  IEEVDVQAPQAGEVMVKLVATGVCHTDAFTLSGA-------DPEGIFPCILGHEGAGIVV 69

Query: 80  EAGEGAEEHFEVAVGDKVIAEQIVPCGKCRFCKSGKYWMCEVHNIFGFQREVAEGG---- 135
           E GEG      VAVGD VI      CG+C+FCKSGK  +C+       +  + +G     
Sbjct: 70  EVGEGVTS---VAVGDHVIPLYTPECGECKFCKSGKTNLCQAIRATQGKGLMPDGTSRFS 126

Query: 136 --------------MAQYMRIPKTAIVHKIPESVSLEDSALVEPMACSIHT-----VNRG 176
                          ++Y  +P+ AI  KI  + +L+   L   + C I T     +N  
Sbjct: 127 LNGQPIYHFMGTSTFSEYTVLPEIAIA-KINPAAALDKVCL---LGCGITTGIGAVLNTA 182

Query: 177 DIQLDDVVVIAGAGTLGLCMVQVAALKTPKKLVVIDMVDERLELAKKFGADVVINPSRDN 236
            ++    V + G G +GL ++Q A L    +++ ID+  ++ E AK+ GA   INP   +
Sbjct: 183 KVEPGSTVAVFGLGGVGLSVIQGAVLAKASRILAIDINPDKAEFAKQLGATDFINPKDYD 242

Query: 237 --AREIINGLTDNYGCDVYIETTGVPAGVTQGLDLIRK-LGRFVEFSVFGAETSVDWS-- 291
              +E+I  LTD  G D   E  G    +   L+   K  G      V GA   +     
Sbjct: 243 RPIQEVIVELTDG-GVDYSFEAIGNVNTMRAALESCHKGWGESTIIGVAGAGQEISTRPF 301

Query: 292 --IIGDRKELDVRGAHLGPYCYPIAIDLFERGLVTSKGIVTHDFPLDDWAEAFELANSTK 349
             + G        G   G    P  ++ +  G +     VT   PL++  EAFE  ++ K
Sbjct: 302 QLVTGRVWRGSAFGGVKGRSQLPGYVEQYLNGQIKVDEFVTETRPLEEINEAFEDMHAGK 361

Query: 350 SIKVLL 355
            I+ ++
Sbjct: 362 VIRTVI 367


Lambda     K      H
   0.322    0.139    0.432 

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: 292
Number of extensions: 18
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: 359
Length of database: 369
Length adjustment: 29
Effective length of query: 330
Effective length of database: 340
Effective search space:   112200
Effective search space used:   112200
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 (21.9 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