GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Pseudomonas stutzeri RCH2

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate GFF356 Psest_0357 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= uniprot:A0A2E7P8M8
         (258 letters)



>FitnessBrowser__psRCH2:GFF356
          Length = 255

 Score =  109 bits (272), Expect = 6e-29
 Identities = 83/252 (32%), Positives = 122/252 (48%), Gaps = 10/252 (3%)

Query: 3   LNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDP--QFWARLTGLQPRAALF 60
           + LQ++V +VTG   GIG  I+L+LA EGA  V+  R + +   +   ++     R    
Sbjct: 1   MRLQNQVALVTGSTQGIGRGIALRLAEEGADIVINGRQDDEQARESLEQVHARGRRVCFI 60

Query: 61  QLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVG-LDAGRNEFVASLERNLIHYYV 119
             ++ D  +C   V E + + GRLD LVNNAGV      LDA  +++   L  NL   + 
Sbjct: 61  AADVGDVEQCQRLVREGIEQMGRLDILVNNAGVQRHAAFLDAQADDYDQVLNVNLRGPFF 120

Query: 120 MAHYCVPHLK--ATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVR 177
           +A     +L+     G I+N SS        N + YCASKG    L R  A  L   G+ 
Sbjct: 121 LAQAFARYLREHGRGGRIINNSSVHEELPHPNFTAYCASKGGLKMLMRNIAIELAPLGIT 180

Query: 178 VNALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSS 237
           VN + P  V TP+  + +    N  EKL ++   IP G R     ++A +  FL S  + 
Sbjct: 181 VNNVAPGAVETPINRELM----NQPEKLASLLQNIPAG-RLGRPHDVAGVVAFLASPDAE 235

Query: 238 HTTGQWVFVDGG 249
           + TG  + VDGG
Sbjct: 236 YITGTTLVVDGG 247


Lambda     K      H
   0.318    0.134    0.394 

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: 152
Number of extensions: 10
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: 258
Length of database: 255
Length adjustment: 24
Effective length of query: 234
Effective length of database: 231
Effective search space:    54054
Effective search space used:    54054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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