GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Pantoea rwandensis LMG 26275

Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate WP_084937098.1 HA51_RS22635 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase

Query= BRENDA::Q97YM2
         (349 letters)



>NCBI__GCF_002095475.1:WP_084937098.1
          Length = 374

 Score =  117 bits (294), Expect = 4e-31
 Identities = 113/374 (30%), Positives = 171/374 (45%), Gaps = 47/374 (12%)

Query: 4   VNMVKSKAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFR 63
           +NM+K++AA+     EPL IE+V++  PQ  EVL+RI   GVC TD     G + +  F 
Sbjct: 1   MNMIKTRAAVAWAAGEPLKIEEVDLMPPQKGEVLVRIVATGVCHTDAYTLSGKDPEGVF- 59

Query: 64  LPIILGHENAGTIVEVGE-LAKVKKGDNVVVYATWGDLTCRYCREGKFNICK-------N 115
            P ILGHE  G +  +GE +  V  GD+V+   T     C++C  GK N+C+        
Sbjct: 60  -PAILGHEGGGVVEAIGEGVTSVAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRSTQGK 118

Query: 116 QIIPGQTT--------------NGGFSEYMLVKSSRWLVKLNSLSPVEAAPLADAG-TTS 160
            ++P  TT                 FSEY +V     L  ++  +P+E   L   G TT 
Sbjct: 119 GLMPDGTTRFFKDGKPIFHYMGTSTFSEYTVVPEIS-LAVISKEAPLEEVCLLGCGVTTG 177

Query: 161 MGAIRQALPFISKFAE-PVVIVNGIGGLAVYTIQILKALMKNITIVGISRSKKHRDFALE 219
           MGA+       +K  E   V + G+GG+ +  I I   + K   I+GI  +    D A +
Sbjct: 178 MGAVMNT----AKVKEGDTVAIFGLGGIGLSAI-IGAKMAKAGRIIGIDLNTSKFDLARK 232

Query: 220 LGADYVSEMKD----AESLINKLTDGLGASIAIDLVGTEETTYNLGKLLAQ---EGAIIL 272
           LGA  +   KD     + +I +LTDG G   + + +G      +  +   +   E  II 
Sbjct: 233 LGATDLINPKDYDKPIQDVIVELTDG-GVDYSFECIGNVNVMRSALECCHKGWGESVIIG 291

Query: 273 VGMEGKRVSLEAFDTA---VWNKKLLGSNYGSLNDLEDVVRLSESGK--IKPYII-KVPL 326
           V   G+ +S   F      VW     G   G    L  +V+    GK  +  +I   +PL
Sbjct: 292 VAGAGEEISTRPFQLVTGRVWRGSAFGGVKGR-TQLPGIVQDYLDGKFALNDFITHTMPL 350

Query: 327 DDINKAFTNLDEGR 340
           ++IN AF  + EG+
Sbjct: 351 EEINDAFDLMHEGK 364


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: 380
Number of extensions: 32
Number of successful extensions: 5
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: 374
Length adjustment: 29
Effective length of query: 320
Effective length of database: 345
Effective search space:   110400
Effective search space used:   110400
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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