GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Paucidesulfovibrio gracilis DSM 16080

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  266 bits (681), Expect = 1e-75
 Identities = 162/496 (32%), Positives = 275/496 (55%), Gaps = 15/496 (3%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           L+ +KG+ K F  V A    +LN+YPGRV AL+GENGAGKST+M +L G Y  DAGT+  
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGRE---FVNRFGKIDWKTMYA 120
            GK   F+  + + EAGIG+++Q   L+  +T+AEN+ LG+E   F+N       K M  
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFFLNP------KEMRN 137

Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
              +L  +  L       V DLS+G++Q VEI K+L  +S+V+I DEPT  LT  ET  L
Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDS-LIEMMVG 239
           F  + ++  QG+ IV+ISH+++E+  + D++ + R G+   E   + +T  + L   MVG
Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVG 257

Query: 240 RKLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299
           +++  +        GD  L+V NL G G+ D++F L +GE++ V G+ G G+  L++ + 
Sbjct: 258 KEVLLEVDREAMPHGDAVLQVRNLTGIGLEDITFDLHQGEVVAVVGVAGNGQKALVEAIC 317

Query: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359
           G        + + G        +    N + YI EDR        +++ +N+ LT  + F
Sbjct: 318 GLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGF 377

Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419
           +R G  L      +  ++ I+ F+++   +      LSGGN QK  +AR L   P++++ 
Sbjct: 378 AR-GPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVA 436

Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFT- 478
           ++PT+G+D+ A ++++  +   + +   I+LV+ ++ E L ++DR+ V++ G     F+ 
Sbjct: 437 EQPTQGLDIAATEQVWNHLLAAR-EMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSV 495

Query: 479 --REQATQEVLMAAAV 492
             +++  +  LM A V
Sbjct: 496 SDKQKVNRIGLMMAGV 511



 Score = 57.8 bits (138), Expect = 9e-13
 Identities = 56/248 (22%), Positives = 115/248 (46%), Gaps = 11/248 (4%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           +A+LQ++ +     G+  L     +++ G V+A+VG  G G+  +++ + G+      T+
Sbjct: 273 DAVLQVRNLT----GI-GLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTM 327

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQE---LNLIPQLTIAENIFLG-REFVNRFGKIDWKT 117
             +GK       K S +  +  I ++   L     L + +N+ L  R+   R   +D K 
Sbjct: 328 FIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKK 387

Query: 118 MYAEADKLLAKLNLR-FKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTE 176
              +  +L+ K ++R  +   L   LS G+ Q   +A+ L    ++I+ ++PT  L    
Sbjct: 388 AARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAA 447

Query: 177 TESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEM 236
           TE ++  +   +    GI+ ++  + E  ++ D V V   G+F+    V+   + + I +
Sbjct: 448 TEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGL 506

Query: 237 MVGRKLED 244
           M+    ED
Sbjct: 507 MMAGVEED 514


Lambda     K      H
   0.318    0.137    0.380 

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: 576
Number of extensions: 40
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 501
Length of database: 514
Length adjustment: 34
Effective length of query: 467
Effective length of database: 480
Effective search space:   224160
Effective search space used:   224160
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 (21.7 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