GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Shewanella loihica PV-4

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__PV4:5210421
          Length = 255

 Score =  140 bits (352), Expect = 3e-38
 Identities = 91/249 (36%), Positives = 137/249 (55%), Gaps = 5/249 (2%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQI--NPSRTLALQ 66
           F+++ ++A+VTGA+ GIG A+AEL +  GA+V++   K E  + VA QI  N     A+ 
Sbjct: 7   FDLSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAMA 66

Query: 67  VDITKKENIEKVVAEIKKVYPKIDILANSAGV-ALLEKAEDLPEEYWDKTMELNLKGSFL 125
             +   E I+    +I+  + ++DIL N+A          D     ++KTME+NL+G F 
Sbjct: 67  CHVGDLEAIQATFEQIQAKHGRLDILVNNAATNPYFGHILDTDLNAFNKTMEVNLRGYFF 126

Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185
           M+   GR M   G G I+N AS  ++   +    Y  SKAA+VSMT+  A E AP  I  
Sbjct: 127 MSVTAGRMMREQGHGVILNTASVNALQPGEMQGIYSISKAAVVSMTKAFAKECAPLGIRC 186

Query: 186 NAISPTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244
           NA+ P    T+     +   ++ + +   IP GR   P E+A   L+LVSDA+S  TGE 
Sbjct: 187 NALLPGFTKTQFAGALFNNDKIYQQLIARIPMGRHAVPSEMAGAVLYLVSDASSYTTGET 246

Query: 245 LIIDGGYTI 253
           L++DGG T+
Sbjct: 247 LVVDGGLTL 255


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: 154
Number of extensions: 10
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: 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.

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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