GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Bacteroides oleiciplenus YIT 12058

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_009130737.1 HMPREF9447_RS15730 ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_000315485.1:WP_009130737.1
          Length = 333

 Score =  132 bits (331), Expect = 1e-35
 Identities = 76/239 (31%), Positives = 127/239 (53%), Gaps = 5/239 (2%)

Query: 3   LRTENLTVSYGTDK----VLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGT 58
           +   NL + Y   K    V   +S  L  G++T L+G NG GKSTLL   +      SG 
Sbjct: 6   ITANNLCIGYRQGKQEKRVHEHLSFQLYPGELTCLLGANGTGKSTLLRTLAASQPALSGE 65

Query: 59  VFLGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNAR 118
           + + D P++  S ++ +R + ++        G+TV ELV+ GR P    +GRL+  D+A 
Sbjct: 66  LLVEDKPLSAYSEKERSRTIGVVLTDKTQAGGLTVYELVALGRQPHTGFFGRLNKADHAI 125

Query: 119 VNVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLM 178
           +  A+    I+H A     ELS G+RQ+  +A  L Q  P++LLDEPT +LD+  ++++M
Sbjct: 126 IEEALEAVSISHKAQSYTAELSDGERQKVMIAKALVQECPLILLDEPTAFLDVVSRIEIM 185

Query: 179 RLMGELRT-QGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFS 236
            L+  L   Q K ++   HD+ QA    D+L +++  + +  G  E+++    +  +FS
Sbjct: 186 TLLHRLAVEQSKAILLSTHDIEQALVLADKLWLLSKENGLQCGVTEDMILSHRMDGLFS 244


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: 169
Number of extensions: 6
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: 333
Length adjustment: 26
Effective length of query: 229
Effective length of database: 307
Effective search space:    70303
Effective search space used:    70303
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: 48 (23.1 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