GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Pseudomonas stutzeri RCH2

Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate GFF3457 Psest_3522 3-hydroxybutyrate dehydrogenase

Query= metacyc::MONOMER-20835
         (262 letters)



>FitnessBrowser__psRCH2:GFF3457
          Length = 256

 Score =  124 bits (311), Expect = 2e-33
 Identities = 84/248 (33%), Positives = 121/248 (48%), Gaps = 3/248 (1%)

Query: 12  GLRVLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPGTVATR--ADVSDA 69
           G   L++G  +GIG  +A    EAGA + +    +++ A+      G       ADVSD 
Sbjct: 5   GKTALVTGSTSGIGLGIALKLAEAGADLILNGFGDASAALAEVGRHGRKVGHHGADVSDP 64

Query: 70  AQIEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAV 129
           AQI  +F       GG+D+LVNNAGI      ++      W A I INL++ +     A+
Sbjct: 65  AQIAELFAYAERDFGGVDILVNNAGIQH-VAPVEEFPVERWDAIIAINLSSAFHTTRLAL 123

Query: 130 PMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPG 189
           P +++   G +++IASV G +G   +  Y A K  +VGL K +A E   + I  NA+ PG
Sbjct: 124 PGMRQRGWGRIINIASVHGLVGSEQKAAYVAAKHGLVGLTKVVALETATTPITCNAICPG 183

Query: 190 IVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNVT 249
            V  P +   I  RA + G  +         K      VT   + AMALFLCS A   V 
Sbjct: 184 WVLTPLVQQQIDERARESGDEQQARHDLLAEKQPSLDFVTPAQLGAMALFLCSEAGDQVR 243

Query: 250 GQAISVDG 257
           G A ++DG
Sbjct: 244 GAAWNMDG 251


Lambda     K      H
   0.318    0.133    0.383 

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: 167
Number of extensions: 5
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: 262
Length of database: 256
Length adjustment: 24
Effective length of query: 238
Effective length of database: 232
Effective search space:    55216
Effective search space used:    55216
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