GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Shewanella sp. ANA-3

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  147 bits (370), Expect = 6e-40
 Identities = 81/223 (36%), Positives = 138/223 (61%), Gaps = 9/223 (4%)

Query: 6   ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65
           IL  + + K Y  V AL+     L+ GE+ A++G+NGAGKS+++K ++GA + D G+I  
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 66  EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125
            G+P  F +PM+A++AGI TVYQ + L P L++A N+FLG E R+ G+       +    
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGL-------IHFKK 116

Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185
           M   ARA L++  L    +++  +   S   +Q +A+AR  A  +KV+++DEPTA+L  K
Sbjct: 117 MYADARAVLTQFKLDI--DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAK 174

Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228
           E + +  ++  ++ +G+ IV I+H +  V++++DRI + R G+
Sbjct: 175 EVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQ 217



 Score = 73.2 bits (178), Expect = 1e-17
 Identities = 49/197 (24%), Positives = 101/197 (51%), Gaps = 9/197 (4%)

Query: 32  GEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETVYQNLA 91
           G+ + + G  G+G+S +  A+ G    D G I L G+ +    P++A  AGI    ++  
Sbjct: 284 GQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRK 343

Query: 92  LSPA---LSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQA 148
           +      LSI +N+ L  + R    +G W+R L     ++ A+  + +L + T  + ++ 
Sbjct: 344 IDGIIGPLSIRENIILALQAR----IG-WWRYLSNTRQQEIAQFFIDKLQIAT-PDADKP 397

Query: 149 VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLPIVLIS 208
           +E LSGG +Q V +AR  A    ++++DEPT  + +     +++LI  +   G+ +++ S
Sbjct: 398 IEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVAS 457

Query: 209 HNMPHVFEVADRIHIHR 225
             +  +   ++++ + R
Sbjct: 458 SELDELVAFSNKVVVLR 474


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: 252
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 260
Length of database: 499
Length adjustment: 29
Effective length of query: 231
Effective length of database: 470
Effective search space:   108570
Effective search space used:   108570
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: 49 (23.5 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