GapMind for catabolism of small carbon sources

 

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

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  499 bits (1285), Expect = e-146
 Identities = 259/494 (52%), Positives = 349/494 (70%), Gaps = 3/494 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           IL  + +SK +PGVKAL++V   L  GE+ ALLGENGAGKSTL+K +TG    D G I  
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
            G+         AQ+ GI TVYQEVNL+PN++VA NLF+G EP+R GL+  K+M   A  
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           ++  +   +DV  PL+ +S+A+QQ++AI R + +SAKVL+LDEPTASLD +EV++LF ++
Sbjct: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
            QL+ +GV+++F+THFLDQVYQ+SDRITVLRNG F+G   T ELPQ +L++ MLGR L  
Sbjct: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243

Query: 249 HAL--QRAGRTLL-SDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305
             +  Q   RT+  ++  + + ++   KG+I   +L V  G+ VGLAGLLGSGR+E    
Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303

Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           +FG+   DSG+  + G+  NL  P  A   GI  CPEDRK DGII   S+RENIILALQA
Sbjct: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363

Query: 366 QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLI 425
           + GW R +S   QQEIA+ FI +L I TP  ++PIE LSGGNQQKV+L+RWL   P  L+
Sbjct: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423

Query: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIP 485
           LDEPTRGID+GAHAEI++LI TLC +G++LLV SSEL+ELV ++++V+++RDR  V E+ 
Sbjct: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483

Query: 486 LAELSVPAIMNAIA 499
            AEL+   +M AIA
Sbjct: 484 GAELTSQHVMQAIA 497


Lambda     K      H
   0.321    0.138    0.391 

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: 603
Number of extensions: 26
Number of successful extensions: 6
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: 500
Length of database: 499
Length adjustment: 34
Effective length of query: 466
Effective length of database: 465
Effective search space:   216690
Effective search space used:   216690
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: 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 (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