GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Nafulsella turpanensis ZLM-10

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_017730539.1 F752_RS0104500 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_000346615.1:WP_017730539.1
          Length = 339

 Score = 81.6 bits (200), Expect = 2e-20
 Identities = 60/197 (30%), Positives = 105/197 (53%), Gaps = 10/197 (5%)

Query: 26  DFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIET 85
           D ++Y GE+L ++G NGAGKS++++ ++G   P  G++ +EG+PI   +  E R   I  
Sbjct: 31  DLEVYQGELLCLMGPNGAGKSTLLRTLAGVQEPLAGQVIMEGQPIHQLAQQE-RARRISL 89

Query: 86  VYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNI 145
           V      +  +++ + + LGR          W  SL  A  E   +A L++L +  +   
Sbjct: 90  VLTEQLSAGNMNVLELVALGRYPHT-----GWGGSLSPADKEMVLQA-LNDLDIGEL--A 141

Query: 146 NQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL-ELILDVRRRGLPI 204
            + +  LS GQRQ   +ARA A   +++I+DEPTA L +    +++ +L L   RR   I
Sbjct: 142 GRKLYELSDGQRQKAMIARALAQDGQLMILDEPTAHLDLINRLQIMRQLRLLALRRQKAI 201

Query: 205 VLISHNMPHVFEVADRI 221
           ++ +H +    + ADR+
Sbjct: 202 LVATHELELALQSADRL 218


Lambda     K      H
   0.321    0.136    0.383 

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: 172
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 339
Length adjustment: 26
Effective length of query: 234
Effective length of database: 313
Effective search space:    73242
Effective search space used:    73242
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.

Links

Downloads

Related tools

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