GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Marinobacter adhaerens HP15

Align Uncharacterized protein (characterized, see rationale)
to candidate GFF2942 HP15_2886 protein of unknown function cysteine-rich region domain protein

Query= uniprot:E4PLR5
         (279 letters)



>FitnessBrowser__Marino:GFF2942
          Length = 259

 Score =  286 bits (731), Expect = 4e-82
 Identities = 137/248 (55%), Positives = 175/248 (70%), Gaps = 2/248 (0%)

Query: 25  YPEKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEA 84
           YP KP  V  +GTC+VD+F+P+AG+  + LLEREG+ V FPQ Q+CCGQPA+TSGY DEA
Sbjct: 8   YPAKPAKVYFYGTCLVDMFYPDAGIAGVELLEREGIEVLFPQNQTCCGQPAYTSGYHDEA 67

Query: 85  KAVARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEF 144
           ++VARAQLD+      P+VVPSGSC GM R HYP LF D  D +K  E +A R +ELT+F
Sbjct: 68  RSVARAQLDLFP-GDWPIVVPSGSCGGMMRKHYPDLFEDTTDEVKAAE-VAGRVWELTDF 125

Query: 145 LLKVCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGF 204
           LL VC ++L D G P+ +A+HTSCSARREM       +LL QL+ V  ++     ECCGF
Sbjct: 126 LLNVCHIKLEDLGEPTTVAMHTSCSARREMGVAEVGPKLLGQLKNVNLVEQIRPEECCGF 185

Query: 205 GGTFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLAS 264
           GGTF+VR PE+S AMV +K  +L+D+G  + VT D GCLMNI G  EK ++   G+H+ S
Sbjct: 186 GGTFAVRHPEISSAMVSEKVDALVDTGTRQFVTTDCGCLMNIAGYAEKNQKPVEGQHILS 245

Query: 265 FLWERTNG 272
           FLW RT G
Sbjct: 246 FLWSRTQG 253


Lambda     K      H
   0.320    0.134    0.406 

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: 282
Number of extensions: 11
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: 279
Length of database: 259
Length adjustment: 25
Effective length of query: 254
Effective length of database: 234
Effective search space:    59436
Effective search space used:    59436
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