GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Sinorhizobium meliloti 1021

Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate SMa1296 SMa1296 alcohol dehydrogenase

Query= BRENDA::Q97YM2
         (349 letters)



>FitnessBrowser__Smeli:SMa1296
          Length = 340

 Score =  136 bits (343), Expect = 7e-37
 Identities = 107/345 (31%), Positives = 177/345 (51%), Gaps = 21/345 (6%)

Query: 11  AALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILGH 70
           AA++++F +PL IE+V +P+P   +VLI+    GVC TDL   KG    +    P I GH
Sbjct: 5   AAVVREFGKPLVIEEVPVPQPGPGQVLIKYEATGVCHTDLHAAKGDWPVRP-NPPFIPGH 63

Query: 71  ENAGTIVEVG-ELAKVKKGDNVVV---YATWGDLTCRYCREGKFNICKNQIIPGQTTNGG 126
           E  G + ++G E+ ++K+GD V V   +   G   C  CR G   +C +Q   G + +G 
Sbjct: 64  EGVGYVAKLGAEVTRLKEGDRVGVPWLHTACG--CCTPCRTGWETLCGSQQNTGYSVDGT 121

Query: 127 FSEYMLVKSSRWLVKLNS-LSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIG 185
           F++Y L     ++ +L + L    AAP+  AG T    +++      ++    V+V+GIG
Sbjct: 122 FAQYGLADPD-FVGRLPARLEFGPAAPVLCAGVTVYKGLKETEVRPGEW----VLVSGIG 176

Query: 186 GLAVYTIQILKALMKNITIVGISRSKKHRDFALELGADYVSEMK--DAESLINKLTDGL- 242
           GL    +Q  KA+  ++    I   K     A +LGAD V + +  DA   + + T GL 
Sbjct: 177 GLGHMAVQYAKAMGMHVAAADIFPDKLA--LAEKLGADLVVDARAPDAVEEVQRRTGGLH 234

Query: 243 GASIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSL 302
           GA +        E  Y++   L  +G + LVG+   ++ L  FDT +    + GS  G+ 
Sbjct: 235 GALVTAVSPKAMEQAYSM---LRSKGTMALVGLPPGQICLPVFDTVLKRITVRGSIVGTR 291

Query: 303 NDLEDVVRLSESGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVI 347
            DLE+ +  +  GK+  +     +++IN  F  ++EG++DGR V+
Sbjct: 292 QDLEEALEFAGEGKVAAHFSWDKIENINAIFERMEEGKIDGRIVL 336


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: 277
Number of extensions: 16
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: 340
Length adjustment: 29
Effective length of query: 320
Effective length of database: 311
Effective search space:    99520
Effective search space used:    99520
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