GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudomonas fluorescens FW300-N2E2

Align L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized)
to candidate Pf6N2E2_5952 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= SwissProt::Q9HK58
         (254 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5952
          Length = 247

 Score =  125 bits (314), Expect = 8e-34
 Identities = 83/251 (33%), Positives = 136/251 (54%), Gaps = 4/251 (1%)

Query: 2   LDFKGKNAVITGGSRGIGRAIALGLAKQGANILISYASHDSEADEVLETASKYGVKAHKV 61
           +  +GK A++TG SRGIG+AIAL L +QGA I+I  A+  S A+ +  T  + G++   +
Sbjct: 1   MSLQGKVALVTGASRGIGQAIALELGRQGA-IVIGTATSASGAERIAATLKENGIQGTGL 59

Query: 62  KVDQSDPYESIRFAEKAIETFGKVHILVDNAGICPFEDFFRISVDLFEKVWKVNVESHYF 121
           +++ +             E FG   ILV+NAGI       R+  D +  V   N+ S Y 
Sbjct: 60  ELNVTSDESVAAVLASIQEQFGAPAILVNNAGITRDNLMMRMKDDEWFDVVDTNLNSLYR 119

Query: 122 ITQRIAKNMIENKINGRILLISSISAHVGGEFQTHYTTTKSALNGFMHSIAIVLGKYGIL 181
           +++ + + M + +  GRI+ I S+   +G   Q +Y   K+ L GF  ++A  +G   I 
Sbjct: 120 LSKGVLRGMTKARW-GRIISIGSVVGAMGNAGQVNYAAAKAGLEGFSRALAREVGSRSIT 178

Query: 182 VNSLEPGTILTDINKEDLSNQEKRAYMERRTVVGRLGLPEDMVAPALFLLSDDNTYVTGT 241
           VNS+ PG I TD+ +E L   ++ A +  +  +GRLG  +++ +   FL SD   YVTG 
Sbjct: 179 VNSVAPGFIDTDMTRE-LPEAQREALL-TQIPLGRLGQAQEIASVVAFLASDGAAYVTGA 236

Query: 242 ELLADGGMLIN 252
            +  +GGM ++
Sbjct: 237 TIPVNGGMYMS 247


Lambda     K      H
   0.318    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: 140
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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: 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