GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Marinobacter adhaerens HP15

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate GFF3984 HP15_3924 short-chain dehydrogenase/reductase SDR

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__Marino:GFF3984
          Length = 255

 Score =  128 bits (321), Expect = 1e-34
 Identities = 76/249 (30%), Positives = 139/249 (55%), Gaps = 5/249 (2%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPS--RTLALQ 66
           F++T KVAV+TG+  GIG+A+A   +  GA VV+   K E  + +A ++       +A+ 
Sbjct: 6   FDMTGKVAVITGSTKGIGRAIAGEMAVCGAKVVISSRKAEACEQMAEELKAQGFEAMAIP 65

Query: 67  VDITKKENIEKVVAEIKKVYPKIDILA-NSAGVALLEKAEDLPEEYWDKTMELNLKGSFL 125
             + +KE+++ +V +  + +  ID+L  N+A   +     ++ ++ WDK M+ N+K +F 
Sbjct: 66  CHVGRKEDLQNLVKKTNEAWGSIDVLVCNAATNPVYGPTAEMTDDAWDKIMDTNVKSTFW 125

Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185
           +  ++  +M   G G +V ++S A +        Y  SKAA  ++ + LA+EW P  I +
Sbjct: 126 LTNMVLPQMAEKGEGAVVLLSSIAGLRGNTVIGTYGVSKAAEAALARNLAVEWGPKGIRI 185

Query: 186 NAISPTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244
           N+I+P +I T+  +  W   +  +  +   P  R G P ++A  A+FL + A++ ITG+ 
Sbjct: 186 NSIAPGLIKTDFARALWEDPERAKQAEDRTPLRRIGDPVDIAGLAVFLSTKASAYITGQV 245

Query: 245 LIIDGGYTI 253
           ++ DGG TI
Sbjct: 246 IVADGGETI 254


Lambda     K      H
   0.316    0.133    0.369 

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: 158
Number of extensions: 5
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: 254
Length of database: 255
Length adjustment: 24
Effective length of query: 230
Effective length of database: 231
Effective search space:    53130
Effective search space used:    53130
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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