GapMind for catabolism of small carbon sources

 

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

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__ANA3:7024900
          Length = 499

 Score =  271 bits (692), Expect = 5e-77
 Identities = 158/479 (32%), Positives = 270/479 (56%), Gaps = 13/479 (2%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           ++E+++I+K +    A + ++L L  GE+HALLGENGAGKSTL+ ++ G      G I  
Sbjct: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124
            G     ++P  + + GI  V+Q   LV   TV +N+ LG E  + G++  KK   + +A
Sbjct: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123

Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184
           +  ++ L +D +A ++D S+  QQ + I + +   A +L+ DEPTA L   E+Q L  I+
Sbjct: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183

Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSF 244
             L  +G +I+ ITH LD++  ++DR+TV+R G+ I     +      L E M+GRS+  
Sbjct: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243

Query: 245 TI------EKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQS 298
            +      E+T T+ +  +LS++D+ V       +I+ ++L V  G+ +G+AG+ G+G+S
Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVK-----GSIQSMNLTVPKGQAVGLAGLLGSGRS 298

Query: 299 ELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLA 358
           E+  A+ GL  + SG + + GQ +            +   PEDR  DG+I  L++ EN+ 
Sbjct: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358

Query: 359 LQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVD 418
           L    +A +     L+ ++  E  +  + +  +   +   P +  SGGNQQK I+AR + 
Sbjct: 359 LA--LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416

Query: 419 RDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHD 477
            +P LL++ +PTRG+D+GA   I K +    DEG ++L+ S ELDE++  S+++ V+ D
Sbjct: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 61/240 (25%), Positives = 120/240 (50%), Gaps = 8/240 (3%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A++ +SL + AGE+  + G +G G+S LV+ +TG +    G +   G+     +   
Sbjct: 16  GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
             +  +  V ++ +   L+  LT+A+NL L  Y    L   G++++ K+    R ++ +F
Sbjct: 76  AQKAGISTVYQEVN---LVPNLTVAQNLFLG-YEPRRL---GLIHFKKMYADARAVLTQF 128

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
            +   +   P   +S   QQ   IAR V     +L++ +PT  LD   ++ +   L   +
Sbjct: 129 KL-DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIEREEIN 509
            +G A++ ++  LD++  +SDRI V+ +GQ  G        + +L   M G S++ + ++
Sbjct: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQEQLVD 247



 Score = 74.3 bits (181), Expect = 9e-18
 Identities = 57/218 (26%), Positives = 109/218 (50%), Gaps = 6/218 (2%)

Query: 24  INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVTIDSPSKSAQLGIG 83
           +NL + KG+   L G  G+G+S + N + GL    SGSI + G  + +  P  +   GI 
Sbjct: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336

Query: 84  MVHQHFML---VEAFTVTENIILGNEVVKNGILDLKKAGQEIKA--LSEKYGLAV-DPNA 137
           +  +   +   +   ++ ENIIL  +        L    Q+  A    +K  +A  D + 
Sbjct: 337 LCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADK 396

Query: 138 KIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKSIILI 197
            I  +S G QQ+V + + L     +L+ DEPT  +      E++ ++++L  EG S+++ 
Sbjct: 397 PIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVA 456

Query: 198 THKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAE 235
           + +LDE+ + +++V V+R   ++  +  +  TSQ + +
Sbjct: 457 SSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494


Lambda     K      H
   0.315    0.135    0.363 

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: 521
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 499
Length adjustment: 34
Effective length of query: 476
Effective length of database: 465
Effective search space:   221340
Effective search space used:   221340
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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