GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Dechlorosoma suillum PS

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Dsui_2068 Dsui_2068 ABC-type metal ion transport system, ATPase component

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__PS:Dsui_2068
          Length = 278

 Score =  108 bits (270), Expect = 1e-28
 Identities = 82/268 (30%), Positives = 136/268 (50%), Gaps = 25/268 (9%)

Query: 5   PILTARGLVKRY----GRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60
           P L  RG+ K +    G+   +   D D+ PGEI  +IG +GAGKS++++  +    PD 
Sbjct: 9   PALALRGVSKSFRTPDGQQVGVHPTDLDVAPGEIHGIIGFSGAGKSTLLRLANLLERPDA 68

Query: 61  GEIRLEGKPIQFRSPMEARQA--GIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWF 118
           G++ + G+ +   SP + R A   I  ++Q+  L    ++ADN+     I          
Sbjct: 69  GQVVVHGQDLMTLSPADLRTARQRIGMIFQHFNLLHNRTVADNVAFPLRI---------- 118

Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEP 178
              D A + ++ +  L  +GL     +  A   LSGGQ+Q VA+ARA A    V++ DEP
Sbjct: 119 AGADEARINERVKTCLEFVGLSEKAGVYPA--QLSGGQKQRVAIARALAPEPHVLLADEP 176

Query: 179 TAALGVKESRRVLELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGR---RLCVIN 234
           T+AL  + ++ +LE++ DV RR G+ I+L+SH M  +  +  R+ +   G+   RL + N
Sbjct: 177 TSALDPRTTQSLLEVLADVNRRLGVTILLVSHEMGVIRRLCHRVSVMEAGQIVERLTIAN 236

Query: 235 ---PKDYTMSDAVAFMTGAKEPPREAIA 259
              P D  ++  +     A+    EA A
Sbjct: 237 GRIPPDSQLAQWLREYGDAEGDAEEAAA 264


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: 167
Number of extensions: 3
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: 260
Length of database: 278
Length adjustment: 25
Effective length of query: 235
Effective length of database: 253
Effective search space:    59455
Effective search space used:    59455
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