GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Escherichia coli BW25113

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate 15740 b1619 7-alpha-hydroxysteroid dehydrogenase (NCBI)

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__Keio:15740
          Length = 255

 Score = 97.4 bits (241), Expect = 4e-25
 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 27/259 (10%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEIKA 62
           L    K  I+TGAG GIGK  A+ FA  GA VVV+D+         ++ AA+ VV+EI+ 
Sbjct: 7   LRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDI---------NADAANHVVDEIQQ 57

Query: 63  AGGTAVA---NYDSVEDGEKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVYR 119
            GG A A   +  S ++   +   A+   G VDIL+NNAG      F  M   D+   Y 
Sbjct: 58  LGGQAFACRCDITSEQELSALADFAISKLGKVDILVNNAGGGGPKPFD-MPMADFRRAYE 116

Query: 120 VHAKGAYKLSRAAWNHMREKNFGRIIMT-SSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178
           ++    + LS+     M EKN G +I+T +S A    N    +Y S K A   L   +A 
Sbjct: 117 LNVFSFFHLSQLVAPEM-EKNGGGVILTITSMAAENKNINMTSYASSKAAASHLVRNMAF 175

Query: 179 EGKSKNIHCNTIAPIA-ASRLTESVMPPEILEQM----------KPDYIVPLVLYLCHQD 227
           +   KNI  N IAP A  +   +SV+ PEI ++M          +P  I    L+LC   
Sbjct: 176 DLGEKNIRVNGIAPGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIANAALFLCSPA 235

Query: 228 TT-ETGGVFEVGAGWVSKV 245
            +  +G +  V  G V ++
Sbjct: 236 ASWVSGQILTVSGGGVQEL 254


Lambda     K      H
   0.313    0.131    0.371 

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: 240
Number of extensions: 11
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: 441
Length of database: 255
Length adjustment: 28
Effective length of query: 413
Effective length of database: 227
Effective search space:    93751
Effective search space used:    93751
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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