GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Streptomyces kebangsaanensis SUK12

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_073948934.1 RH94_RS20265 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_001906585.1:WP_073948934.1
          Length = 285

 Score =  226 bits (577), Expect = 3e-64
 Identities = 114/250 (45%), Positives = 162/250 (64%), Gaps = 1/250 (0%)

Query: 3   LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62
           L  +++T++Y    +   +S+ +P    T ++GPN CGKSTLL   SR+L P  G V L 
Sbjct: 18  LTADDVTLAYDHRVIAEQLSVEIPDNSFTVIVGPNACGKSTLLRALSRMLKPSRGRVLLD 77

Query: 63  DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122
              I  + ++++AR L LLPQ  + P+GITV +LV  GR P   +  + SAED   V  +
Sbjct: 78  GQVIQSMPAKKVARTLGLLPQSSIAPDGITVGDLVGRGRYPHQGILRQWSAEDERVVQES 137

Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMG 182
           M +TR+  LA R + ELSGGQRQR ++AM LAQ TP++LLDEPTTYLDI HQ+D++ L  
Sbjct: 138 MERTRVAELADRYVDELSGGQRQRVWIAMALAQQTPLLLLDEPTTYLDIQHQIDVLDLCA 197

Query: 183 EL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241
           EL   QG+T+VAVLHDLN A+RY   LV +  G V+AQG P +++T  L+  VF +  ++
Sbjct: 198 ELHEEQGRTLVAVLHDLNHAARYATHLVALRGGKVVAQGAPNDIVTAELVEEVFGLRCQV 257

Query: 242 HPEPVSGRPM 251
             +P +G P+
Sbjct: 258 VEDPETGTPL 267


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: 186
Number of extensions: 11
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: 285
Length adjustment: 25
Effective length of query: 230
Effective length of database: 260
Effective search space:    59800
Effective search space used:    59800
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 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