GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas simiae WCS417

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate GFF2165 PS417_11045 3-oxoacyl-ACP reductase

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>FitnessBrowser__WCS417:GFF2165
          Length = 255

 Score = 95.1 bits (235), Expect = 1e-24
 Identities = 81/254 (31%), Positives = 122/254 (48%), Gaps = 21/254 (8%)

Query: 12  GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEA----TSRFPKLHAGIADVS 67
           G  V +S GA+GIG  +  AF    A+V   D  Q+  +      +SR   +     D++
Sbjct: 13  GKTVLISGGASGIGEFMVRAFAAQGAKVGFVDRAQSQGERLAALLSSRGHTVEFVNCDIT 72

Query: 68  KQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRK 127
            +      I      LG + VLVNNA        +EE+D   ++  ++ NL   F+  + 
Sbjct: 73  DEIAYKAAIGRFEHSLGPISVLVNNAA-NDARHTLEEVDSEMFDRLIAVNLKHAFFAAKA 131

Query: 128 AVPVLKETSDCASIIAMSSVAGRL---GYPFRTPYASTKWAIVGLVKSLAAELGPSNVRV 184
            VP++K     A II + SV   +   GYP    YA++K A  G+ ++LA ELGPS +RV
Sbjct: 132 VVPMMKSAGGGA-IINLGSVGWMMASAGYPV---YAASKAAAHGMTRALARELGPSRIRV 187

Query: 185 NAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASP 244
           N ++PG V  E+    ++   D      +A +E   +   L   V  + IA MALFLAS 
Sbjct: 188 NTLVPGWVMTEKQ---LAMWVD------DAAKELISRSQCLPGSVLPEHIANMALFLASD 238

Query: 245 AGSNVTGQAISVDG 258
           A +  + Q   VDG
Sbjct: 239 ASAMCSAQNFIVDG 252


Lambda     K      H
   0.318    0.134    0.375 

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: 112
Number of extensions: 5
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: 255
Length adjustment: 24
Effective length of query: 239
Effective length of database: 231
Effective search space:    55209
Effective search space used:    55209
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