GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldE in Fibrella aestuarina BUZ 2

Align Uncharacterized protein (characterized, see rationale)
to candidate WP_041258297.1 FAES_RS22450 (Fe-S)-binding protein

Query= uniprot:B2TBW0
         (256 letters)



>NCBI__GCF_000331105.1:WP_041258297.1
          Length = 243

 Score =  264 bits (674), Expect = 1e-75
 Identities = 125/244 (51%), Positives = 164/244 (67%), Gaps = 1/244 (0%)

Query: 10  MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69
           M V LFIPC++D FYP+VGIA+L+LL++ G+ V YP +QTCCGQPMAN+G   ++ G   
Sbjct: 1   MNVGLFIPCYVDQFYPQVGIASLQLLQKLGVSVTYPAQQTCCGQPMANAGCERDSVGVYD 60

Query: 70  VFARNFAGYDYIVGPSASCIHHVREHLTALEQTDEVKKVRANAYELVEFLHDVVGAREFP 129
            F   FA +DY+V PSASC++HVR+H   ++QT  V+ VR   Y+LV+F+ +V+   +  
Sbjct: 61  HFVNTFADFDYVVAPSASCVYHVRKHFDIIDQTPAVQHVRERTYDLVQFITEVLKVEQIE 120

Query: 130 WAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDECCGF 189
            A FPHRVGLH SC   R L+ A+ SE+      + R LL GV G+E V   R DECCGF
Sbjct: 121 -AHFPHRVGLHLSCHGQRGLRMATDSELTPVRDGQMRRLLTGVDGLELVDLDRYDECCGF 179

Query: 190 GGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFIHIAQ 249
           GG F V+E  VS RMGQD+V DH+  GAE I  GD+SCLMH +G   R     R +HIA+
Sbjct: 180 GGLFCVSEAAVSARMGQDRVADHVRNGAEVITGGDVSCLMHLEGIVRRKNLPIRVLHIAE 239

Query: 250 VLNG 253
           +LNG
Sbjct: 240 ILNG 243


Lambda     K      H
   0.323    0.137    0.422 

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: 224
Number of extensions: 7
Number of successful extensions: 2
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: 243
Length adjustment: 24
Effective length of query: 232
Effective length of database: 219
Effective search space:    50808
Effective search space used:    50808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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