GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Bacteroides thetaiotaomicron VPI-5482

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 350961 BT1433 putative oxidoreductase (NCBI ptt file)

Query= SwissProt::Q92EU6
         (254 letters)



>FitnessBrowser__Btheta:350961
          Length = 270

 Score =  131 bits (330), Expect = 1e-35
 Identities = 91/263 (34%), Positives = 141/263 (53%), Gaps = 23/263 (8%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED-----VKDVAAQINPSRTLA 64
           FN+ DKV V+TG A  +GK +A   +++GA VV+LD  E+     V+ + A+ N +  + 
Sbjct: 5   FNVKDKVVVITGGAGILGKGIAAYLAKEGAKVVVLDRSEEAGKALVESIKAEGNEA--MF 62

Query: 65  LQVDITKKENIEKVVAEIKKVYPKIDILANSAG-------VALLEKAEDLPEEYWDKTME 117
           L  D+  KE +E    EI K Y +ID+L N+AG       +A  +   DL  + + K ++
Sbjct: 63  LYTDVMDKEVLEGNKVEIMKAYGRIDVLLNAAGGNMAGATIAPDKTFFDLQIDAFKKVVD 122

Query: 118 LNLKGSFLMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAME 177
           LNL G+ L   +    M+    G IVN  S++++  L + V Y A+KAAI + T+ +A E
Sbjct: 123 LNLFGTVLPTMVFAEIMVEQKKGSIVNFCSESALRPLTRVVGYGAAKAAIANFTKYMAGE 182

Query: 178 WA---PYNINVNAISPTVILTELGKKAWAGQVGE--DMKKLI----PAGRFGYPEEVAAC 228
            A      + VNAI+P   LT+  +       G   D  K I    P  RFG PE++   
Sbjct: 183 LALKFGNGLRVNAIAPGFFLTDQNRALLTNPDGSLTDRSKTILAHTPFNRFGEPEDLYGT 242

Query: 229 ALFLVSDAASLITGENLIIDGGY 251
             +L+SDA++ +TG   +IDGG+
Sbjct: 243 IHYLISDASNFVTGTVAVIDGGF 265


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: 182
Number of extensions: 13
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: 270
Length adjustment: 25
Effective length of query: 229
Effective length of database: 245
Effective search space:    56105
Effective search space used:    56105
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