GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          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.

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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, 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