GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Paucidesulfovibrio gracilis DSM 16080

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  240 bits (613), Expect = 8e-68
 Identities = 152/481 (31%), Positives = 264/481 (54%), Gaps = 21/481 (4%)

Query: 3   QSTPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTG 62
           Q  P +S +G+ K F  V A  DIS + Y G+V AL+GENGAGKSTL+ +L+G Y P  G
Sbjct: 20  QGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAG 79

Query: 63  SVVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGG--IVNRSLL 120
           ++ ++G+ + FS    A+ AG+ ++YQ   LV  MTVAEN+ LGQ   +G   +  + + 
Sbjct: 80  TIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQ---EGSFFLNPKEMR 136

Query: 121 NYEAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREID 180
           N    L +++ G+DIDP   +  LS+G+ Q VEI K L R+++++ FDEPT+ L+ RE  
Sbjct: 137 NRVQELSVRY-GLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETF 195

Query: 181 NLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAM 240
           +LF  + ++ ++G+ I+++SH++EE+ A++D I + + GR    F++ +      L   M
Sbjct: 196 HLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255

Query: 241 VGRDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMK 300
           VG+++      +   +G+  L++  +   G+   I+  +  GE+V + G+ G G+  L++
Sbjct: 256 VGKEVLLEVDREAMPHGDAVLQVRNLTGIGLE-DITFDLHQGEVVAVVGVAGNGQKALVE 314

Query: 301 GMFG------GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDN 354
            + G       T    G+ + D       KPS      +   PEDR         ++ DN
Sbjct: 315 AICGLRKPPVDTMFIMGKRWRD----FYAKPSW--KNSLAYIPEDRLGLATCRNLNLVDN 368

Query: 355 INISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWL 414
           + ++ R+    G   ++      +    I+  +I+      L   LSGGN QK++L R L
Sbjct: 369 LLLTTRQGFARGPW-LDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLAREL 427

Query: 415 SEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMRE 474
               ++I+ ++PT+G+D+ A  +++N + A A +   +L  + DL E L +ADR+ V+  
Sbjct: 428 YRCPRLIVAEQPTQGLDIAATEQVWNHLLA-AREMAGILLVTGDLNEALQLADRVAVIYR 486

Query: 475 G 475
           G
Sbjct: 487 G 487



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 61/222 (27%), Positives = 108/222 (48%), Gaps = 9/222 (4%)

Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMM 334
           ISL +  G +  L G  GAG+S LM  + G  Q  AG + +D +P+       AI AG+ 
Sbjct: 43  ISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIG 102

Query: 335 LCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAE 394
           +  +      ++   +V +N+ +       L    + N  +E +  +    L+I  P A 
Sbjct: 103 MVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRY---GLDID-PAAR 155

Query: 395 QLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLF 454
             + +LS G +Q+  + + L  + +V++ DEPT  +       ++  ++ +A QG +++F
Sbjct: 156 --VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVF 213

Query: 455 ASSDLPEVLGVADRIVVMREGEIAGELLHEQADERQALSLAM 496
            S  L EVL VAD I ++R+G I GE    +   +  L+  M
Sbjct: 214 ISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRM 255



 Score = 52.0 bits (123), Expect = 5e-11
 Identities = 53/230 (23%), Positives = 104/230 (45%), Gaps = 9/230 (3%)

Query: 23  LTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNA 82
           L DI+FD + G+V A++G  G G+  L++ + G   P   ++ I G+         +   
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 83  GVAIIYQE---LHLVPEMTVAENIYLG--QLPHKGGIVNRSLLNYEAGLQLKHLGMDIDP 137
            +A I ++   L     + + +N+ L   Q   +G  +++     +    +K   +    
Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGR 405

Query: 138 DTPLKY-LSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVI 196
              L + LS G  Q   +A+ L R  ++I  ++PT  L     + ++  +   R+   ++
Sbjct: 406 IAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREMAGIL 465

Query: 197 LYVSHRMEEIFALSDAITVFKDGRYVKTF--TDMQQVDHDALVQAMVGRD 244
           L V+  + E   L+D + V   GR++  F  +D Q+V+   L+ A V  D
Sbjct: 466 L-VTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVEED 514


Lambda     K      H
   0.319    0.136    0.391 

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: 582
Number of extensions: 30
Number of successful extensions: 7
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: 504
Length of database: 514
Length adjustment: 34
Effective length of query: 470
Effective length of database: 480
Effective search space:   225600
Effective search space used:   225600
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 (21.7 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