GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Bacteroides thetaiotaomicron VPI-5482

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)

Query= BRENDA::Q4J9F2
         (255 letters)



>FitnessBrowser__Btheta:353297
          Length = 248

 Score =  157 bits (397), Expect = 2e-43
 Identities = 94/251 (37%), Positives = 142/251 (56%), Gaps = 8/251 (3%)

Query: 6   LKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVEL-LEDRLNQIVQELRGMGKEVLGVKA 64
           L  K  IVTGA  GIG+AIA KFA   + +   +L +++   +   EL  MG +  G  +
Sbjct: 4   LDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYAS 63

Query: 65  DVSKKKDVEEFVRRTFETYSRIDVLCNNAGIM-DGVTPVAEVSDELWERVLAVNLYSAFY 123
           + +  +D  + V    + + RID+L NNAGI  DG+  +  +S++ W+ V+ VNL SAF 
Sbjct: 64  NAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGL--MMRMSEQQWDMVINVNLKSAFN 121

Query: 124 SSRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRA 183
              A  P+M++Q  G I+N AS+ G+ G    A Y  +K G+I L +SIA   G +GIRA
Sbjct: 122 FIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIRA 181

Query: 184 VAVLPGTVKTNIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNG 243
            A+ PG + T++    S   E+      K+     R   PED+AN+  FLASD +S+V+G
Sbjct: 182 NAIAPGFILTDMTAALS--DEVRAEWAKKIP--LRRGGTPEDVANIATFLASDMSSYVSG 237

Query: 244 DAVVVDGGLTV 254
             + VDGG+ +
Sbjct: 238 QVIQVDGGMNM 248


Lambda     K      H
   0.318    0.135    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: 156
Number of extensions: 7
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: 255
Length of database: 248
Length adjustment: 24
Effective length of query: 231
Effective length of database: 224
Effective search space:    51744
Effective search space used:    51744
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 (21.7 bits)
S2: 46 (22.3 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