GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Pseudomonas fluorescens FW300-N1B4

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate Pf1N1B4_5706 Fumarylacetoacetate hydrolase family protein

Query= reanno::Smeli:SM_b21112
         (281 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5706
          Length = 373

 Score =  125 bits (314), Expect = 1e-33
 Identities = 92/276 (33%), Positives = 134/276 (48%), Gaps = 42/276 (15%)

Query: 41  SKLDELANLDVETLPAVSGNPRLGPCVAGTGKFICIGLNYSDHAAETGATVPPEP--IIF 98
           + +D+LA L    L    G  +L   V    +F+C G NY  H  E+G     +   +IF
Sbjct: 97  NSIDDLAQLKGTEL--AEGEVKLLSPVTRNQQFVCQGANYRQHMIESGMDPDAKKFNMIF 154

Query: 99  MKATSAIVGPNDDLVLPRGSEKTDWEVELGIVIGKT---AKYVSEAEALDYVAGYCTVHD 155
            KATS +V  + DL+ PR     D+E+ELG+V+ +    A  V++A   +++AG   V+D
Sbjct: 155 TKATSCLVAADSDLIKPRTVRFLDYEIELGLVMKRAINGAVAVTDANLHEFIAGVVIVND 214

Query: 156 VSERAFQTERHGQWTKGKSCDTFGPTGPWLVTKD--EVADPQDLAMWLKVNGETMQDGST 213
            S R  Q  +  Q+ KGKS  TFGP GP+L   D   +   ++L + L VN +  Q+ ST
Sbjct: 215 YSARDIQIPQM-QFYKGKSFRTFGPVGPYLCLLDATNIHYLKELQLRLTVNDQVRQNDST 273

Query: 214 KTMVYGAAHLVSYLSQFMSLRPGDIISTGTPPGVGMGMKPP------------------- 254
             +VYG A  ++ LS       GD+I+TGTP G  + +  P                   
Sbjct: 274 ANLVYGPAETLTELSALQDFAAGDLIATGTPAGCALTVPSPAKQRIAALMPEATKWKLFL 333

Query: 255 -------RYLKAGDVVEL------GIEGLGSQKQRV 277
                  +YLK GDVVE       G+  LG Q+ RV
Sbjct: 334 KAQEGRTQYLKPGDVVEARIRSADGVIDLGVQRNRV 369


Lambda     K      H
   0.315    0.136    0.408 

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: 295
Number of extensions: 26
Number of successful extensions: 6
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: 281
Length of database: 373
Length adjustment: 28
Effective length of query: 253
Effective length of database: 345
Effective search space:    87285
Effective search space used:    87285
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: 42 (22.0 bits)
S2: 48 (23.1 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