GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Shewanella sp. ANA-3

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

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          Length = 499

 Score =  450 bits (1157), Expect = e-131
 Identities = 231/489 (47%), Positives = 340/489 (69%), Gaps = 2/489 (0%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           I+ +K I+  +PGVKAL+ V L L+ GEVHAL+GENGAGKST++K +TG    + G I+ 
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126
            G+PQ FN  +DAQ AGI+TVYQEVNL  NL+V +N+ LG+E R    I +KK +  A+ 
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123

Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186
            L Q  L+ ID   PLS  SIA+QQL+AIAR + ++AKVL+LDEPT+SLDA EV+ LF I
Sbjct: 124 VLTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182

Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246
           + +++  GVAI+F++HFLDQ+Y+I+DR+T+LRNGQFI E +T + P+ +LI  M+G+S  
Sbjct: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242

Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELG 306
           E   +  ++  R +T  E  ++ ++ +  KG+I  +++ + KG+ VG AGLLGSGR+E+ 
Sbjct: 243 E-QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301

Query: 307 RLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIAL 366
             ++G D  DSG+  L G+K+N+S P  A+   IA   E+R+ +GIIG L++R+NI++AL
Sbjct: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361

Query: 367 QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426
           QA  G ++ +       I   ++ +L +   D D+P++ LSGGNQQKV++ RWLA  P L
Sbjct: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421

Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486
           L+LDEPTRGIDIGA AEI +++  L  +GM ++  SSEL+E+V  S+ + VL+DR+ + E
Sbjct: 422 LVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRE 481

Query: 487 IENDDTVSQ 495
           +   +  SQ
Sbjct: 482 LSGAELTSQ 490


Lambda     K      H
   0.316    0.135    0.376 

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: 643
Number of extensions: 31
Number of successful extensions: 7
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: 513
Length of database: 499
Length adjustment: 34
Effective length of query: 479
Effective length of database: 465
Effective search space:   222735
Effective search space used:   222735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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