GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudomonas fluorescens GW456-L13

Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate PfGW456L13_2119 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= SwissProt::A3LZU7
         (258 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2119
          Length = 272

 Score =  127 bits (320), Expect = 2e-34
 Identities = 87/259 (33%), Positives = 137/259 (52%), Gaps = 23/259 (8%)

Query: 5   LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64
           L  KVV +TG   GIG AI    A   A+++++ +  E+  ++A   +++ +D    V+ 
Sbjct: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGAD----VVA 74

Query: 65  IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124
           I  D+S  +    +  LA++  G I+V V+ AGV  FR+ LE+T E   +   I+L+GA+
Sbjct: 75  IKADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAW 134

Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTP-------TKAGILSLMQSTAC 177
           +  +A   QM++QG  GSII I+S        H TH  P        K G+L L ++   
Sbjct: 135 YGCKAVLPQMIEQGI-GSIINIAS-------THSTHIIPGCFPYPVAKHGLLGLTRALGI 186

Query: 178 ALGKYGIRCNAILPGTISTALNEE---DLKDPE-KRKYMEGRIPLGRVGDPKDIAGPAIF 233
                G+R NAI PG I T LN +      DP  +R+      P  R+G P ++A  A+F
Sbjct: 187 EYAPKGVRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVF 246

Query: 234 LASDMSNYVNGAQLLVDGG 252
           LASD + ++N + + +DGG
Sbjct: 247 LASDEAPFINASCITIDGG 265


Lambda     K      H
   0.317    0.136    0.382 

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: 121
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: 258
Length of database: 272
Length adjustment: 25
Effective length of query: 233
Effective length of database: 247
Effective search space:    57551
Effective search space used:    57551
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: 41 (21.6 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