GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pseudomonas fluorescens GW456-L13

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate PfGW456L13_2522 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2522
          Length = 248

 Score =  139 bits (349), Expect = 8e-38
 Identities = 90/250 (36%), Positives = 128/250 (51%), Gaps = 14/250 (5%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           RL+NKV ++TG A GIG A V  F+++ A+++  DI +   +               +  
Sbjct: 3   RLQNKVAVVTGGASGIGLACVRRFSAEGAQVIGLDIGSAPADFPGLF----------MTL 52

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137
           DV ++  +  + +  + R GRIDVLVN AGV       + T  +W+R   I+L G+    
Sbjct: 53  DVRDEAQVQQVMQEVISRFGRIDVLVNAAGVADQGSVTQTTTANWQRVMDINLTGSMLTS 112

Query: 138 KAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197
           K  L  M+EQ  GSIIN+ S        G   Y V+K G+  LTR++ I+Y    +RVN 
Sbjct: 113 KYALASMVEQRNGSIINVGSIFGLQGCDGNVAYNVSKGGINQLTRSMAIDYGYANIRVNG 172

Query: 198 IAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257
           + PG IET +     +   D  A        H   R GQP EVA  A+FLASDEA F++ 
Sbjct: 173 LCPGLIETPMT----SMVRDNDAFHAFFASQHMLNRSGQPEEVANVALFLASDEASFVSG 228

Query: 258 SCITIDGGRS 267
             I +DGG S
Sbjct: 229 QMIAVDGGFS 238


Lambda     K      H
   0.321    0.137    0.419 

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: 152
Number of extensions: 6
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
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: 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