GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Paucidesulfovibrio gracilis DSM 16080

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  226 bits (577), Expect = 1e-63
 Identities = 153/481 (31%), Positives = 255/481 (53%), Gaps = 19/481 (3%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           L+  + + K +  V A  D  L++  G V AL G NGAGKST +S+L G  Q DAG+I L
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G PV+F+   +A+ AGI M+ Q    +  MTVAEN+ LG+E       ++ K +  R +
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE---GSFFLNPKEMRNRVQ 140

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
           EL      D+D  + +  LS+ + Q VEI K    D +V+I DEPT+ +   E   LF+A
Sbjct: 141 ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEA 200

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFR----DGAFVESGRMADIDRDHLVRGIVG 241
           + ++  QG  IV++SH+L E+  +AD+ +I R    +G F ES   +  D   L   +VG
Sbjct: 201 LWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKAD---LACRMVG 257

Query: 242 QELTRIDHKVGRECA--ANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFL 299
           +E+     +V RE     +  LQV NL+  G   DI+  L QGE++ + G+ G+G+   +
Sbjct: 258 KEVLL---EVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGNGQKALV 313

Query: 300 NCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSA 359
             I GL      ++ + GK       K +    ++ + EDR         +++ N+ L+ 
Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT 373

Query: 360 YKRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVC 419
            +  +    ++ +K  +   +++K+  I+   +      +SGGN QK VLA+ L   P  
Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433

Query: 420 LLCDEPTRGIDEGAKQEIY-HLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVT 478
           ++ ++PT+G+D  A ++++ HLL    R     ++V+ +  E L L+DR+AV   GR + 
Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLL--AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMD 491

Query: 479 I 479
           +
Sbjct: 492 V 492



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 49/216 (22%), Positives = 103/216 (47%), Gaps = 8/216 (3%)

Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333
           DISL +  G +  + G  G+G+S  ++ + G    D+G++ L GKP+     +  I AG+
Sbjct: 42  DISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGI 101

Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSLE 393
            +V +      LV + ++  N+ L           +N ++     +++  R  +      
Sbjct: 102 GMVYQHFM---LVESMTVAENVLLGQEGSF----FLNPKEMRNRVQELSVRYGLDIDPAA 154

Query: 394 LPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIV 453
             V+ +S G +Q+V + K L  +   L+ DEPT  +       ++  L +    G + + 
Sbjct: 155 R-VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVF 213

Query: 454 VSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEA 489
           +S +  E+L ++D IA+ + GR+    +++ ++ +A
Sbjct: 214 ISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249



 Score = 39.3 bits (90), Expect = 3e-07
 Identities = 42/213 (19%), Positives = 92/213 (43%), Gaps = 6/213 (2%)

Query: 22  LRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAA 81
           L D    L  G V A+ G  G G+   +  + G+ +    ++ + G   +      +   
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 82  GIAMITQE---LEPIPYMTVAENIWLG-REPRRAGCIVDNKALNRRTRELLDSLEFDVDA 137
            +A I ++   L     + + +N+ L  R+    G  +D K   R T EL+   +     
Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGR 405

Query: 138 TSPMH-RLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGI 196
            + +  +LS   +Q   +A+      ++++ ++PT  +     + ++  +     + AGI
Sbjct: 406 IAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGI 464

Query: 197 VYVSHRLSELAQIADDYSIFRDGAFVESGRMAD 229
           + V+  L+E  Q+AD  ++   G F++   ++D
Sbjct: 465 LLVTGDLNEALQLADRVAVIYRGRFMDVFSVSD 497


Lambda     K      H
   0.319    0.135    0.381 

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: 491
Number of extensions: 28
Number of successful extensions: 8
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: 495
Length of database: 514
Length adjustment: 34
Effective length of query: 461
Effective length of database: 480
Effective search space:   221280
Effective search space used:   221280
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