GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter related (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  208 bits (529), Expect = 4e-58
 Identities = 142/471 (30%), Positives = 251/471 (53%), Gaps = 11/471 (2%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           ++ +K ++K +  V A +D+SL ++ G V ALLGENGAGKSTL+ ++ G    D G I  
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+P  F++  DA +AGI  VYQ   LV ++TVA+N+ LG E      ++ K+M    + 
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGS--FFLNPKEMRNRVQE 141

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +  ++ LDID +A +SD S+  +Q + I + +   ++VL+ DEPTA L  +E   LF  L
Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAEL-PQPKLIEAMLGRSLQ 242
            ++  +G +IVFI+H L++V  ++D I +LR G+  GE+  +E+  +  L   M+G+ + 
Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEVL 261

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
            + VD++     +   +AVL       +   ++ +   + +G+ V + G+ G+G+  +  
Sbjct: 262 LE-VDRE----AMPHGDAVLQVRNLTGI--GLEDITFDLHQGEVVAVVGVAGNGQKALVE 314

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362
           A+ GL      ++ + G++        +    +A  PEDR        L++ +N++L  +
Sbjct: 315 AICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTR 374

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
                  +L   +        I K  I          QLSGGN QK +LAR L   P L+
Sbjct: 375 QGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLI 434

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
           V ++PT+G+DI A  ++   +     E   +L+ + +L+E +  +++V V+
Sbjct: 435 VAEQPTQGLDIAATEQVWNHL-LAAREMAGILLVTGDLNEALQLADRVAVI 484



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 53/214 (24%), Positives = 108/214 (50%), Gaps = 8/214 (3%)

Query: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336
           ++L +  G+   L G  G+G+S + + + G    D+G+I L G+ +  S   DAI AGI 
Sbjct: 43  ISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIG 102

Query: 337 LCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADK 396
           +  +   +   +  +++ EN++L  +            R QE++  +   L I   D   
Sbjct: 103 MVYQHFML---VESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRY--GLDI---DPAA 154

Query: 397 PIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVA 456
            +  LS G +Q+V + + L  +  +L+ DEPT  +       + + +  + ++G S++  
Sbjct: 155 RVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFI 214

Query: 457 SSELDELVAFSNKVVVLRDRYAVRELSGAELTSQ 490
           S +L+E++A ++++ +LR      E S +E+TS+
Sbjct: 215 SHKLEEVLAVADEIAILRQGRIEGEFSESEVTSK 248



 Score = 55.5 bits (132), Expect = 5e-12
 Identities = 55/230 (23%), Positives = 108/230 (46%), Gaps = 19/230 (8%)

Query: 20  LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGE--------PQHFN 71
           LED++  L  GEV A++G  G G+  LV+ + G +   +  +  +G+        P   N
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 72  TP--MDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFK 129
           +   +   + G++T  + +NLV NL +         P     +  KK   D   ++ +F 
Sbjct: 346 SLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKKFD 400

Query: 130 LDIDVSAPLS-DYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKA 188
           +     A L+   S    Q   +AR +    +++V ++PT  LD    + ++  L  L A
Sbjct: 401 IRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL--LAA 458

Query: 189 KGVA-IVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAML 237
           + +A I+ +T  L++  Q++DR+ V+  G+F+  +  ++  +   I  M+
Sbjct: 459 REMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508


Lambda     K      H
   0.319    0.136    0.377 

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: 533
Number of extensions: 28
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 514
Length adjustment: 34
Effective length of query: 465
Effective length of database: 480
Effective search space:   223200
Effective search space used:   223200
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 Apr 09 2024. 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