GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Dinoroseobacter shibae DFL-12

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 3606961 Dshi_0388 ABC transporter related (RefSeq)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Dino:3606961
          Length = 261

 Score =  427 bits (1097), Expect = e-124
 Identities = 215/256 (83%), Positives = 235/256 (91%)

Query: 2   AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61
           +Q+PIL  R LVKRYGRVTALD  DF+LYPGEILAVIGDNGAGKSS+IKA+SGAV PDEG
Sbjct: 5   SQQPILAGRNLVKRYGRVTALDHCDFELYPGEILAVIGDNGAGKSSLIKAVSGAVIPDEG 64

Query: 62  EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121
           E+ LEGK ++F+SP++AR AGIETVYQ LA+SPALSIADNMF+GRE+RKPG  GKW R L
Sbjct: 65  EVFLEGKRVRFQSPLDARAAGIETVYQQLAMSPALSIADNMFMGRELRKPGWRGKWLRQL 124

Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181
           DRAAMEK AR KLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKV+I+DEPTAA
Sbjct: 125 DRAAMEKFARDKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVIILDEPTAA 184

Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241
           LGVKESRRVLELILDVR RG+PIVLISHNMPHVFEVADRIHIHRLG+RLCVI+PKD+ MS
Sbjct: 185 LGVKESRRVLELILDVRARGIPIVLISHNMPHVFEVADRIHIHRLGKRLCVIDPKDHDMS 244

Query: 242 DAVAFMTGAKEPPREA 257
           DAVAFMTGAKEP   A
Sbjct: 245 DAVAFMTGAKEPESAA 260


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: 280
Number of extensions: 4
Number of successful extensions: 1
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 17 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