GapMind for catabolism of small carbon sources

 

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

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate 5210113 Shew_2557 short-chain dehydrogenase/reductase SDR (RefSeq)

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__PV4:5210113
          Length = 306

 Score =  152 bits (384), Expect = 1e-41
 Identities = 93/292 (31%), Positives = 147/292 (50%), Gaps = 9/292 (3%)

Query: 3   LNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLG-GSHTGQGSSSKAADKVVEEIK 61
           + F ++V +VTGAG G+G+ YA+  A+RGA++ + D G G    Q  +    +K    + 
Sbjct: 2   MRFDEQVAVVTGAGAGLGRAYAIALAERGARLAIIDSGSGDSRCQSYAGAGLNKTARTLA 61

Query: 62  AAGGTAVANYDSVEDGEKI---VQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLVY 118
             G   ++    V D + +   ++T +  +G +DI INNAGI   VSF  ++   W    
Sbjct: 62  ELGADCLSFQLDVTDSQALKSAIETVLKRWGRIDIAINNAGIHTPVSFDSLSFEQWQRQL 121

Query: 119 RVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLAQ 178
            V   G++ L++  W  M+ +N+GRI+MT+ A+GLYG+  +  Y + KMALVGL N+LA+
Sbjct: 122 DVDLNGSFHLTKLVWPQMKRQNYGRIVMTAGASGLYGDMHETPYSTSKMALVGLVNSLAK 181

Query: 179 EGKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEVG 238
           EG+  NI  NT+ P A + +T   + P +        +   +LYLC   T  +G      
Sbjct: 182 EGRDYNISVNTLVPEALTAMTAHHLSPLVKPLFSTSSVNATLLYLC-SSTACSGQHLLAA 240

Query: 239 AGWVSK---VRLQRSAGVYMKDLTPEKIKDNWAQIESFDNPSYPTSASESVS 287
           AG VS    V  Q    +      PE I   W ++       +  S  E V+
Sbjct: 241 AGSVSHGMFVEFQ-PLRIVEDGCKPEVIAQRWDELYRAQPCHFHESGEEQVT 291


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: 298
Number of extensions: 14
Number of successful extensions: 2
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: 306
Length adjustment: 30
Effective length of query: 411
Effective length of database: 276
Effective search space:   113436
Effective search space used:   113436
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