GapMind for catabolism of small carbon sources

 

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

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Btheta:351439
          Length = 259

 Score = 97.1 bits (240), Expect = 3e-25
 Identities = 80/256 (31%), Positives = 122/256 (47%), Gaps = 24/256 (9%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT----S 67
           V VITG A G+G AT  R+V +G   V+ DL     + +A KL      A ADV     S
Sbjct: 8   VVVITGAAGGIGEATTRRIVSEGGKVVIADL----SQERADKLAAELTQAGADVRPIYFS 63

Query: 68  EKDVQTALAL---AKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124
             ++Q+   L   A  ++G++DV +N  G     +  N++K     ++ F  V  +NL  
Sbjct: 64  ATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLD---IDYFDEVFHLNLCC 120

Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184
           T  + + V   M  +    GG  G I+N AS++          Y ASK G++ +T  IA 
Sbjct: 121 TMYLSQQVIPIMTTH----GG--GNIVNVASISGLTADANGTLYGASKAGVINLTKYIAT 174

Query: 185 DLAPIGIRVMTIAPGLFGTP-LLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN 243
            +    IR   +APGL  TP  L +L E+V N    Q   P  LG+P + A  +  +  N
Sbjct: 175 QMGKKNIRCNAVAPGLVLTPAALDNLNEEVRNIFLGQCATP-YLGEPEDVAATIAFLASN 233

Query: 244 P--FLNGEVIRLDGAI 257
              ++ G+ I +DG +
Sbjct: 234 DARYITGQTIVVDGGL 249


Lambda     K      H
   0.318    0.135    0.385 

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: 155
Number of extensions: 7
Number of successful extensions: 1
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: 261
Length of database: 259
Length adjustment: 24
Effective length of query: 237
Effective length of database: 235
Effective search space:    55695
Effective search space used:    55695
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: 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