GapMind for catabolism of small carbon sources

 

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

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_3499 Short-chain dehydrogenase/reductase SDR

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3499
          Length = 255

 Score =  154 bits (390), Expect = 1e-42
 Identities = 92/246 (37%), Positives = 137/246 (55%), Gaps = 6/246 (2%)

Query: 6   KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65
           K   V+GASRGIG A A+  A+QGA V++    S     G   +A+ I A GG A A+  
Sbjct: 12  KIAFVSGASRGIGEAIAKLLAQQGAHVIV----SSRKLEGCQHVADAIIAAGGKATAIAC 67

Query: 66  DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICP-FHSFLDMPRELYLKTVGTNLNGAYFT 124
              +++   ++ A   E FG +D+LVNNA   P F + LD     + KTV  N+ G +F 
Sbjct: 68  HIGEMEQISQVFAGIKEQFGRLDILVNNAATNPQFCNVLDTDLSAFQKTVDVNIRGYFFM 127

Query: 125 VQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRC 184
              A + M+E G GG+II V+SI+ +  G  Q  Y+ TKA ++++ +  A     +GIRC
Sbjct: 128 SVEAGKLMRENG-GGSIINVASINGVSPGIFQGIYSVTKAAVINMTKVFAKECAQFGIRC 186

Query: 185 NAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGAS 244
           NA+LPG   T      + +         ++PL R+ +P ++AG +++LASD + Y TG S
Sbjct: 187 NALLPGLTDTKFASALVKNEAILNTALQQIPLKRVADPSEMAGAVLYLASDASSYTTGVS 246

Query: 245 LLVDGG 250
           L VDGG
Sbjct: 247 LNVDGG 252


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: 163
Number of extensions: 8
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: 255
Length adjustment: 24
Effective length of query: 232
Effective length of database: 231
Effective search space:    53592
Effective search space used:    53592
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