GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Escherichia coli BW25113

Align Lmo2664 protein (characterized, see rationale)
to candidate 16198 b2091 galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding (NCBI)

Query= uniprot:Q8Y413
         (350 letters)



>FitnessBrowser__Keio:16198
          Length = 346

 Score =  214 bits (546), Expect = 2e-60
 Identities = 119/347 (34%), Positives = 188/347 (54%), Gaps = 3/347 (0%)

Query: 1   MRAAVLYENNVIK-AEQIDEATCGKDQVRVEVKAVGICGSDIHKMQTRWKYPLPAVMGHE 59
           M++ V   + +++ AE +      +D+VRV++ + G+CGSD+ ++     +  P  +GHE
Sbjct: 1   MKSVVNDTDGIVRVAESVIPEIKHQDEVRVKIASSGLCGSDLPRIFKNGAHYYPITLGHE 60

Query: 60  FAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALCDNYRMVGSHFHGGFAEN 119
           F+G I  +GS V ++  GD VA +PL PC  C  C  G ++ C  Y  +GS   GGFAE 
Sbjct: 61  FSGYIDAVGSGVDDLHPGDAVACVPLLPCFTCPECLKGFYSQCAKYDFIGSRRDGGFAEY 120

Query: 120 VVMKADNVISI-GDLDFEEGAMIEPLAVSMHGVLGIQPRLGDTVIVFGIGTIGILVVQCL 178
           +V+K  NV ++  D+  E+GA IEP+ V +H     Q      VI+ G GTIG+L +QC 
Sbjct: 121 IVVKRKNVFALPTDMPIEDGAFIEPITVGLHAFHLAQGCENKNVIIIGAGTIGLLAIQCA 180

Query: 179 LLAGVKDIIAVDISDKKLADAREFGCKYTINPKNEDLKERVFAYTNGLGADIALECAGSK 238
           +  G K + A+DIS +KLA A+ FG   T N       +            + LE AG  
Sbjct: 181 VALGAKSVTAIDISSEKLALAKSFGAMQTFNSSEMSAPQMQSVLRELRFNQLILETAGVP 240

Query: 239 ITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAFENIFRRELTLKGFWNSYSAPFPGEEWR 298
            T E  + +     ++  +G  + D+ L    F  I R+ELT+ G W +YS+P+PG+EW 
Sbjct: 241 QTVELAVEIAGPHAQLALVGTLHQDLHLTSATFGKILRKELTVIGSWMNYSSPWPGQEWE 300

Query: 299 TSIEFVKQGRIKLKPLISHRYKLEETKEAFDMILSREHDYNKVMILP 345
           T+   + + ++ L+PLI+HR   E   +A   I +R     KV+++P
Sbjct: 301 TASRLLTERKLSLEPLIAHRGSFESFAQAVRDI-ARNAMPGKVLLIP 346


Lambda     K      H
   0.321    0.139    0.417 

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: 293
Number of extensions: 14
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: 350
Length of database: 346
Length adjustment: 29
Effective length of query: 321
Effective length of database: 317
Effective search space:   101757
Effective search space used:   101757
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