Alignments for a candidate for fruK in Paucidesulfovibrio gracilis DSM 16080

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Paucidesulfovibrio gracilis DSM 16080

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  249 bits (637), Expect = 1e-70
 Identities = 155/474 (32%), Positives = 258/474 (54%), Gaps = 13/474 (2%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P+V +KG+T  F  V A D + L +YPG V AL+GENGAGKST++  L G Y+ +AG+I 
Sbjct: 23  PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           +DGKP +F+   DA  AGI  VYQ   L  +++V ENV+LG E  G F ++ K+     +
Sbjct: 83  LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE--GSFFLNPKEMRNRVQ 140

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           +   + GL+ IDP   +S +S+  +Q V I + +  +++VLI DEPT+ L   E   LF 
Sbjct: 141 ELSVRYGLD-IDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFE 199

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKD-TPRDELIGMMIGKS 244
            + K+ + G +I+F+SH L+++  + D + ILR G+   E    + T + +L   M+GK 
Sbjct: 200 ALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKE 259

Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
                     +  RE  P    ++ V+ L   G +  +  D+++GEVV   G+ G+G+  
Sbjct: 260 V-------LLEVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGNGQKA 311

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
           L   + G  KP   T  + GK+        + KN +AY  E+R       +L +  N+L+
Sbjct: 312 LVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLL 371

Query: 365 ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424
             +        + KK+A     + +K+ ++RP         LSGGN QK ++ R L   P
Sbjct: 372 TTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCP 431

Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
            L++ ++PT+G+DI A  ++   +L  A +  G++ ++ +L E ++L+D + V+
Sbjct: 432 RLIVAEQPTQGLDIAATEQVWNHLL-AAREMAGILLVTGDLNEALQLADRVAVI 484



 Score =  105 bits (263), Expect = 3e-27
 Identities = 75/251 (29%), Positives = 130/251 (51%), Gaps = 18/251 (7%)

Query: 255 KARREITPGEKPIVDVKGL----GKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLY 310
           +++R++ P   P+V +KGL    GK    + + ++IY G V    G  G+G++ L  +L 
Sbjct: 12  RSKRDVPPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLA 71

Query: 311 GADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATR 370
           G  +PD+GT  L+GK V  S    A++  I    ++     ++  +TV +N+L+  +   
Sbjct: 72  GRYQPDAGTIALDGKPVRFSSARDAIEAGIGMVYQHFM---LVESMTVAENVLLGQE--- 125

Query: 371 GMFKPIPKKEADAIVDKYMKELNVR---PADPDRPVKNLSGGNQQKVLIGRWLATHPELL 427
           G F   PK+  + +     +EL+VR     DP   V +LS G +Q+V I + L     +L
Sbjct: 126 GSFFLNPKEMRNRV-----QELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVL 180

Query: 428 ILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEI 487
           I DEPT  +       + + +  +A QG  +VFIS +LEEV+ ++D+I +L+      E 
Sbjct: 181 IFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEF 240

Query: 488 ENDDTVSQATI 498
              +  S+A +
Sbjct: 241 SESEVTSKADL 251



 Score = 59.3 bits (142), Expect = 3e-13
 Identities = 47/225 (20%), Positives = 106/225 (47%), Gaps = 8/225 (3%)

Query: 23  LDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNA 82
           L+ +   L+ GEV A++G  G G+  +++A+ G+ K    ++ + GK  +      +   
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345

Query: 83  GIATVYQE---VNLCTNLSVGENVMLGHEK---RGPFGIDWKKTHEAAKKYLAQMGLESI 136
            +A + ++   +  C NL++ +N++L   +   RGP+ +D KK      + + +  +   
Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPW-LDKKKAARDTTELIKKFDIRPG 404

Query: 137 DPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVA 196
                   +S    Q   +AR +    ++++ ++PT  LD      ++  +   R+    
Sbjct: 405 RIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREMA-G 463

Query: 197 ILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
           IL V+  L++  ++ DR+ ++  G+F+      D  +   IG+M+
Sbjct: 464 ILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508


Lambda     K      H
   0.316    0.135    0.376 

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: 597
Number of extensions: 35
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: 513
Length of database: 514
Length adjustment: 35
Effective length of query: 478
Effective length of database: 479
Effective search space:   228962
Effective search space used:   228962
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources