GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas fluorescens FW300-N2E3

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AO353_21770 AO353_21770 3-hydroxybutyrate dehydrogenase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21770
          Length = 257

 Score =  119 bits (298), Expect = 6e-32
 Identities = 83/250 (33%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAA--IDRARTAHPQLHAGVADVSDC 69
           G   L++G+ +GIG  IA +    GAN+ +     A+  I + +    ++    ADVSD 
Sbjct: 6   GKTALVTGSTSGIGLGIALSLAKAGANLILNGFGDASTVIAQVQQFGGKVGHHPADVSDP 65

Query: 70  AQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRKAV 129
           AQ+  +I  A  + GG+D+L+NNAGI     AVED     W+  I  NL+S F+  R ++
Sbjct: 66  AQIAEMIAYAEREFGGVDILVNNAGIQH-VSAVEDFPVERWDSIIAINLSSVFHSTRLSL 124

Query: 130 PLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNAILP 189
           P ++       I+ +ASV G++G   +  Y A+K  ++G+ K + +E   +NV  NAI P
Sbjct: 125 PGMRAKGWGR-IVNIASVHGQVGSVGKAAYVAAKHGVIGLTKVVGLETATSNVTCNAICP 183

Query: 190 GVVEGERMDRVISARAESLGIGFDQMKGEYL-QKISLRRMVTVHDVAAMALFLASPAGQN 248
           G V    + + I  RA + GI   Q + + L +K      VT   +  + LFL S AG  
Sbjct: 184 GWVLTPLVQKQIDDRA-AAGIDPQQAQHDLLAEKQPSLEFVTPSQLGELVLFLCSEAGSQ 242

Query: 249 ISGQAISVDG 258
           + G A ++DG
Sbjct: 243 VRGAAWNIDG 252


Lambda     K      H
   0.320    0.136    0.391 

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: 157
Number of extensions: 8
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: 263
Length of database: 257
Length adjustment: 24
Effective length of query: 239
Effective length of database: 233
Effective search space:    55687
Effective search space used:    55687
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 (21.8 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