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_086510236.1 BZY95_RS12370 ATP-binding cassette domain-containing protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_002151265.1:WP_086510236.1
          Length = 255

 Score =  175 bits (444), Expect = 7e-49
 Identities = 90/231 (38%), Positives = 140/231 (60%), Gaps = 1/231 (0%)

Query: 16  KVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPINMLSSRQLA 75
           ++L  VS +   GK+  LIG NG GKSTL+   ++      G + L   P+     R+ A
Sbjct: 15  RLLQPVSHAFSEGKVYGLIGHNGSGKSTLIKLLAQQQPASRGKILLDGKPLEDWGQREFA 74

Query: 76  RRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHLAVRR 135
           RR++ LPQH  + E +  +EL+ +GR PW  L GR + +D A +  A+  +     A R 
Sbjct: 75  RRVAYLPQHLPSAENLIGRELIGFGRYPWHGLLGRQTPKDKAAIERAIELSHTEAFADRL 134

Query: 136 LTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQGK-TVVAV 194
           +  LSGG+RQR +LAM+LAQ +  +LLDEP   LDI HQ++++ L+ +L  + +  V+ V
Sbjct: 135 VDTLSGGERQRVWLAMLLAQESRFLLLDEPLAALDIAHQMEVLSLIRKLCDELRLCVIIV 194

Query: 195 LHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPEP 245
           LHD+N ASRYCD+L+ + +G V+A G+PE +MT   L  ++ +  ++ P P
Sbjct: 195 LHDINMASRYCDELLALHSGRVLAHGSPERIMTGSTLEAIYGLPMQVMPHP 245


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: 204
Number of extensions: 9
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: 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