GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Flavobacterium sp. LM5

Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_078212710.1 BXU11_RS12070 phosphate ABC transporter ATP-binding protein

Query= CharProtDB::CH_088321
         (255 letters)



>NCBI__GCF_002017945.1:WP_078212710.1
          Length = 252

 Score = 96.7 bits (239), Expect = 4e-25
 Identities = 75/235 (31%), Positives = 125/235 (53%), Gaps = 22/235 (9%)

Query: 7   NLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRL--LMPQ---SGTVF- 60
           +L++ YG  K L+ VS+ +   K+TALIGP+GCGKST L C +R+  L+P    SG +  
Sbjct: 10  DLSLFYGEKKALSSVSMQIQANKVTALIGPSGCGKSTFLRCINRMNDLIPGVKISGRMLV 69

Query: 61  ----LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDN 116
               + D  +++++ R   +++ ++ Q    P   ++ E V+YG  P ++     +  D 
Sbjct: 70  EGIDIYDKEVDVVNIR---KKIGMVFQKS-NPFPKSIFENVAYG--PRINGIKNKTQLDE 123

Query: 117 ARVNVAMNQTRINHLAVRRLTE----LSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDIN 172
             V V++ Q  I      RL +    LSGGQ+QR  +A  LA N  ++L+DEP + LD  
Sbjct: 124 I-VEVSLRQAAIWEELKDRLDDSAMGLSGGQQQRLCIARTLAVNPDIILMDEPASALDPL 182

Query: 173 HQVDLMRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMT 227
               +  L+ EL+ Q  T+V V H++ QA+R  D       G ++  G  +++ T
Sbjct: 183 STSKIEELVHELKEQ-YTIVIVTHNMQQAARTSDHTAFFYMGELIEMGKTKDIFT 236


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: 150
Number of extensions: 6
Number of successful extensions: 3
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: 252
Length adjustment: 24
Effective length of query: 231
Effective length of database: 228
Effective search space:    52668
Effective search space used:    52668
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