GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolG in Rhizobium freirei PRF 81

Align D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) (characterized)
to candidate WP_037154101.1 RHSP_RS23475 Gfo/Idh/MocA family oxidoreductase

Query= BRENDA::Q9WYP5
         (334 letters)



>NCBI__GCF_000359745.1:WP_037154101.1
          Length = 339

 Score =  197 bits (502), Expect = 2e-55
 Identities = 117/334 (35%), Positives = 191/334 (57%), Gaps = 5/334 (1%)

Query: 1   MRIGVIGLGRIGTIHAENL-KMIDDAILYAISDVREDRLREMKEKLGVEKAYKDPHELIE 59
           + +G+IG GRIG+ H E + + + DA L AI+D       ++ +KLG + +Y D  +L+ 
Sbjct: 7   VNVGLIGAGRIGSFHGETIARRLVDAELVAIADPAPGAAAKLADKLGADTSYTDVADLLA 66

Query: 60  DPNVDAVLVCSSTNTHSELVIACAKAKKHVFCEKPLSLNLADVDRMIEETKKADVILFTG 119
            P +DAV++ +    HS +V+  A+A K +FCEKP++L L D DR I   + A V L  G
Sbjct: 67  HPGLDAVIIATPARFHSNIVVQAAEAGKAIFCEKPMALTLEDADRAIAAARSAGVPLQVG 126

Query: 120 FNRRFDRNFKKLKEAVENGTIGKPHVLRITSRDPAPPPLDYIRVS-GGIFLDMTIHDFDM 178
           FNRR+D+ F + + A++ G +G P ++R  +RDP P   D  R+    IF +  IHDFD 
Sbjct: 127 FNRRWDQAFAEGRAAIDAGKVGAPQLIRSLTRDPGPFGADPDRIPLWTIFYETLIHDFDT 186

Query: 179 ARYI-MGEEVEEVFADGSVLVDEEIGKAGDVDTAVVVLRFKSGALGVIDNSRRAVYGYDQ 237
             ++  G +  EVFA    LV  +  + G +DTAVV +RF +G++ V + +  A+YGYD 
Sbjct: 187 LLWLNPGAKPVEVFAMADALVRPDAREKGFLDTAVVNIRFDNGSIAVAEANFSALYGYDI 246

Query: 238 RIEVFGSKGRIFADNVRETTVVLTDEQGDRGSRYLYFFLERYRDSYLEELKTFIKNVKSG 297
           R EVFGS G +   +VR +++   D+ G     +     + +  +Y  +L +F+  V+ G
Sbjct: 247 RGEVFGSGGMVTMGDVRRSSMTRFDKDGVSNDTWRR-DTDHFIHAYTAQLASFVNAVRDG 305

Query: 298 E-PPAVSGEDGKMALLLGYAAKKSLEEKRSVKLE 330
                 +G D + AL +  A+ +S+ +K+ V L+
Sbjct: 306 ALKDGPTGLDARNALAIALASIQSVSKKQPVILK 339


Lambda     K      H
   0.319    0.139    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: 252
Number of extensions: 12
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: 334
Length of database: 339
Length adjustment: 28
Effective length of query: 306
Effective length of database: 311
Effective search space:    95166
Effective search space used:    95166
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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