GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Halomonas desiderata SP1

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_086509933.1 BZY95_RS10800 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_002151265.1:WP_086509933.1
          Length = 255

 Score =  158 bits (399), Expect = 1e-43
 Identities = 85/229 (37%), Positives = 131/229 (57%), Gaps = 3/229 (1%)

Query: 21  VSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQLARRLSL 80
           ++LS+  G++  ++GPNG GK+TLL+  + L  P++G V +   P+  L  RQ+AR+L L
Sbjct: 22  LTLSVEPGQVWGVLGPNGAGKTTLLHTLAGLRGPRAGQVLIDGRPLAALGRRQVARKLGL 81

Query: 81  LPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVRRLTELS 140
           + Q        TV+E    GR+PWLS W     ED      A+ +  ++HLA R ++ LS
Sbjct: 82  VFQERHDGFPATVRETALIGRHPWLSAWQMEGGEDLRLAEAALERLDVDHLAERLVSTLS 141

Query: 141 GGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGKTVVAVLHDLNQ 200
           GG+RQR  +A VL Q   + L DEPT +LD++HQ  +M L+ E   +G+ V+  LHDLN 
Sbjct: 142 GGERQRLAIATVLTQAPQIWLADEPTNHLDLHHQSAVMALLAEQAAEGRAVMMCLHDLNL 201

Query: 201 ASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFS---VEAEIHPEPV 246
           A+R+CD L+++        G   +++ P  L  ++      AEI   PV
Sbjct: 202 AARWCDHLLLLYPDGEACWGPARDMLVPAALERLYGQRLATAEIDGAPV 250


Lambda     K      H
   0.320    0.134    0.393 

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: 171
Number of extensions: 4
Number of successful extensions: 1
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: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
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 Apr 09 2024. 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