Alignments for a candidate for fruK in Maridesulfovibrio bastinii DSM 16055

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Maridesulfovibrio bastinii DSM 16055

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_027178119.1 G496_RS0103835 ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_000429985.1:WP_027178119.1
          Length = 513

 Score =  244 bits (622), Expect = 7e-69
 Identities = 164/495 (33%), Positives = 267/495 (53%), Gaps = 18/495 (3%)

Query: 5   NPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSI 64
           +PIV +KGIT  F  V A + + L LYPG + AL+GENGAGKST++  L G ++ + G I
Sbjct: 22  SPIVSLKGITKRFGKVVANNKIVLDLYPGRIKALLGENGAGKSTLMSMLAGRFQPDEGHI 81

Query: 65  MVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAA 124
            VDGK   F+ + DA NAGI  VYQ   L  +++V ENV+LG E  G F ++ K+     
Sbjct: 82  EVDGKRVDFSSSKDAINAGIGMVYQHFMLVDSMTVTENVLLGQE--GGFFVNPKEMSRRV 139

Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184
           KK      LE IDP   ++ +S+  +Q V I + +   ++VLI DEPT+ L   E   LF
Sbjct: 140 KKLAEDYELE-IDPDARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLTPRETFRLF 198

Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEV-MTKDTPRDELIGMMIGK 243
             +  +   G +I+F+SH L+++  I D + ILR G    EV   K T + +L   M+GK
Sbjct: 199 EALWAMTRQGKSIVFISHKLEEVMAIADEVAILRRGCVDSEVPREKITSKADLACRMVGK 258

Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
                 ++  +  R E+  G+K +++VK L   G  N +++++++GEVVG  G+ G+G+ 
Sbjct: 259 ------EVLLEIDRNEVEIGDK-VLEVKSLNGLGLKN-INIEVHRGEVVGIVGVAGNGQQ 310

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
            L   + G   P   +  + GK            + ++Y  E+R D     +L +  N+L
Sbjct: 311 ALVEGVCGLRMPPKDSVFIMGKAWREFFAKMTWNHSLSYIPEDRLDLATARELDLVDNLL 370

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           +  +        + + +A  +  K +++ +VRP         LSGGN QK+++ R L   
Sbjct: 371 LTTRQGFCSGPVLHRDKAAEVAKKLVEDHDVRPGRIQALAWQLSGGNLQKLVLARELYRE 430

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV-----L 478
           P L++ ++PT+G+DI A  E+   +L+ A +  GV+ ++ +L E ++LSD I V     +
Sbjct: 431 PHLIVAEQPTQGLDISATEEVWNRLLE-ARKMAGVLLVTGDLNEALQLSDRIAVMYRGEI 489

Query: 479 KDRHKIAEIENDDTV 493
            D+  + + E  D V
Sbjct: 490 MDQFSVNDTEKVDKV 504



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 67/237 (28%), Positives = 120/237 (50%), Gaps = 12/237 (5%)

Query: 266 PIVDVKGL----GKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           PIV +KG+    GK    N + +D+Y G +    G  G+G++ L  +L G  +PD G   
Sbjct: 23  PIVSLKGITKRFGKVVANNKIVLDLYPGRIKALLGENGAGKSTLMSMLAGRFQPDEGHIE 82

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381
           ++GK+V+ S    A+   I    ++     ++  +TV +N+L+  +   G F  +  KE 
Sbjct: 83  VDGKRVDFSSSKDAINAGIGMVYQHFM---LVDSMTVTENVLLGQEG--GFF--VNPKEM 135

Query: 382 DAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAK 441
              V K  ++  +   DPD  +  LS G +Q+V I + L     +LI DEPT  +     
Sbjct: 136 SRRVKKLAEDYELE-IDPDARINQLSMGEKQRVEILKLLYRESRVLIFDEPTAVLTPRET 194

Query: 442 AEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATI 498
             + + +  +  QG  +VFIS +LEEV+ ++D++ +L+     +E+  +   S+A +
Sbjct: 195 FRLFEALWAMTRQGKSIVFISHKLEEVMAIADEVAILRRGCVDSEVPREKITSKADL 251



 Score = 55.1 bits (131), Expect = 6e-12
 Identities = 46/233 (19%), Positives = 112/233 (48%), Gaps = 13/233 (5%)

Query: 20  VKALDG-----VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFN 74
           VK+L+G     +++ ++ GEV  ++G  G G+  +++ + G+      S+ + GK  +  
Sbjct: 278 VKSLNGLGLKNINIEVHRGEVVGIVGVAGNGQQALVEGVCGLRMPPKDSVFIMGKAWREF 337

Query: 75  GTLDAQNAGIATVYQE-VNLCT--NLSVGENVMLGHEK---RGPFGIDWKKTHEAAKKYL 128
                 N  ++ + ++ ++L T   L + +N++L   +    GP  +   K  E AKK +
Sbjct: 338 FAKMTWNHSLSYIPEDRLDLATARELDLVDNLLLTTRQGFCSGPV-LHRDKAAEVAKKLV 396

Query: 129 AQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMR 188
               +           +S    Q + +AR +     +++ ++PT  LD +   +++  + 
Sbjct: 397 EDHDVRPGRIQALAWQLSGGNLQKLVLARELYREPHLIVAEQPTQGLDISATEEVWNRLL 456

Query: 189 KVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
           + R     +L V+  L++  +++DR+ ++  G+ + +    DT + + +G+M+
Sbjct: 457 EARKMA-GVLLVTGDLNEALQLSDRIAVMYRGEIMDQFSVNDTEKVDKVGLMM 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: 587
Number of extensions: 32
Number of successful extensions: 9
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: 513
Length adjustment: 35
Effective length of query: 478
Effective length of database: 478
Effective search space:   228484
Effective search space used:   228484
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.

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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:

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