GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Paucidesulfovibrio gracilis DSM 16080

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  210 bits (535), Expect = 8e-59
 Identities = 145/472 (30%), Positives = 245/472 (51%), Gaps = 16/472 (3%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ++  +GL+K F  V A D++  ++  G + ALLGENGAGKSTL+  L G Y  D GTI L
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +G+ +   +   A + GIG VYQ   L+ +M+VA+N+ +G+E   F  L  KEM  R  E
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFF--LNPKEMRNRVQE 141

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L   YG  +D    ++  S+  +Q V I + +   ++VLI DEPTA L  +E   LF+ +
Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCEL-PQIELVKMMLGRELD 247
            ++ ++G S++F++H L++V  V+D I +LR G   G     E+  + +L   M+G+E+ 
Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEV- 260

Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
              L+     +     V   +N    G +     ++  GE+V + G+ G+G+    E I 
Sbjct: 261 --LLEVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGNGQKALVEAIC 317

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ--- 364
           G++     T  I GK         +    + + PEDR         ++ +N++L  +   
Sbjct: 318 GLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGF 377

Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424
           A+  WL    +K+        I++  IR          LSGGN QK +L+R L   P+ +
Sbjct: 378 ARGPWL---DKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLI 434

Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLA-LLVISSELEELVGYADRVIIM 475
           + ++PT+G+D+ A  ++      L A  +A +L+++ +L E +  ADRV ++
Sbjct: 435 VAEQPTQGLDIAATEQVWN--HLLAAREMAGILLVTGDLNEALQLADRVAVI 484



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 59/227 (25%), Positives = 104/227 (45%), Gaps = 10/227 (4%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K +GK        L + PG +  L G  G+G++    ++ G    D+GT  + GKP    
Sbjct: 32  KRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFS 91

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPIS-RKEQQEIAERFI 386
           S   A   GIG   +      ++ + +V EN++L  Q    +L P   R   QE++ R+ 
Sbjct: 92  SARDAIEAGIGMVYQHFM---LVESMTVAENVLLG-QEGSFFLNPKEMRNRVQELSVRYG 147

Query: 387 RQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIE 446
             +    P+    +  LS G +Q+V + + L    + LI DEPT  +       +   + 
Sbjct: 148 LDID---PAAR--VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALW 202

Query: 447 TLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPA 493
            +   G +++ IS +LEE++  AD + I+R  +   E   +E++  A
Sbjct: 203 KIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKA 249



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 53/234 (22%), Positives = 114/234 (48%), Gaps = 27/234 (11%)

Query: 25  LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAI-------SPKN 77
           L+++ F L +GE++A++G  G G+  L++A+ G+      T+++ G+         S KN
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 78  TAH---AQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASYG 134
           +       +LG+ T  + +NL+ N+ +       R P     L +K+  +  TEL+  + 
Sbjct: 346 SLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKKF- 399

Query: 135 FSLDVREPLNRFSVAMQ------QIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
              D+R P    ++A Q      Q   + R +    ++++ ++PT  LD    E +++ +
Sbjct: 400 ---DIR-PGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL 455

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242
              R+    ++ VT  L++  Q++DR+ V+  G F+      +  ++  + +M+
Sbjct: 456 LAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508


Lambda     K      H
   0.321    0.138    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: 565
Number of extensions: 36
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: 500
Length of database: 514
Length adjustment: 34
Effective length of query: 466
Effective length of database: 480
Effective search space:   223680
Effective search space used:   223680
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