GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudomonas putida KT2440

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PP_1914 PP_1914 3-oxoacyl-[acyl-carrier-protein] reductase subunit

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__Putida:PP_1914
          Length = 246

 Score =  157 bits (398), Expect = 1e-43
 Identities = 99/253 (39%), Positives = 146/253 (57%), Gaps = 7/253 (2%)

Query: 1   MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60
           M L  K  +VTGASRGIG+A A E  RQGA V+    G+    +GA  +A  +   G T 
Sbjct: 1   MSLQGKVALVTGASRGIGQAIALELGRQGATVI----GTATSASGAERIAATLKEHGITG 56

Query: 61  IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120
             +  +    +S E ++AA  E FG+  +LVNNAGI   +  L M  + +   + TNLN 
Sbjct: 57  TGMELNVTSAESVEAVLAAIGEQFGAPAILVNNAGITRDNLMLRMKDDEWFDVIDTNLNS 116

Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180
            Y   +   R M +  R G II++ S+   +G A Q +Y   KAGL    ++ A  +G  
Sbjct: 117 LYRLSKGVLRGMTK-ARWGRIISIGSVVGAMGNAGQANYAAAKAGLEGFSRALAREVGSR 175

Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240
           GI  N+V PG I TD+ +E L + + RE + +++PLGRLG+ D++A  + FLASD A YV
Sbjct: 176 GITVNSVTPGFIDTDMTRE-LPEAQ-REALQTQIPLGRLGQADEIAKVVSFLASDGAAYV 233

Query: 241 TGASLLVDGGLFV 253
           TGA++ V+GG+++
Sbjct: 234 TGATVPVNGGMYM 246


Lambda     K      H
   0.319    0.136    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: 164
Number of extensions: 10
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: 256
Length of database: 246
Length adjustment: 24
Effective length of query: 232
Effective length of database: 222
Effective search space:    51504
Effective search space used:    51504
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: 46 (22.3 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