GapMind for catabolism of small carbon sources

 

Aligments for a candidate for LRA1 in Pseudomonas fluorescens FW300-N1B4

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate Pf1N1B4_451 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_451
           3-oxoacyl-[acyl-carrier protein] reductase (EC
           1.1.1.100)
          Length = 247

 Score =  144 bits (363), Expect = 2e-39
 Identities = 93/254 (36%), Positives = 143/254 (56%), Gaps = 7/254 (2%)

Query: 1   MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60
           M L  K  +VTGASRGIG+A A E  RQGA V+    G+    +GA  +A  +   G   
Sbjct: 1   MSLQGKVALVTGASRGIGQAIALELGRQGAVVI----GTATSASGAERIAATLKENGIQG 56

Query: 61  IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120
             +  +    +S   ++A+  E FG+  +LVNNAGI   +  + M  + +   V TNLN 
Sbjct: 57  TGLELNVTSDESVAAVLASIQEQFGAPAILVNNAGITRDNLMMRMKDDEWHDVVDTNLNS 116

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

Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240
            I  N+V PG I TD+ +E L + + RE + +++PLGRLG+  ++A  + FLASD A YV
Sbjct: 176 SITVNSVAPGFIDTDMTRE-LPEAQ-REALQTQIPLGRLGQAQEIASVVAFLASDGAAYV 233

Query: 241 TGASLLVDGGLFVN 254
           TGA++ V+GG++++
Sbjct: 234 TGATIPVNGGMYMS 247


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: 161
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: 247
Length adjustment: 24
Effective length of query: 232
Effective length of database: 223
Effective search space:    51736
Effective search space used:    51736
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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