Alignments for a candidate for fruK in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Desulfovibrio vulgaris Miyazaki F

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  243 bits (621), Expect = 1e-68
 Identities = 162/496 (32%), Positives = 262/496 (52%), Gaps = 17/496 (3%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P+V + GI   F  V+A   + L + PG + AL+GENGAGKST++  L G  + +AG+I+
Sbjct: 28  PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           VDG P  F    DA  AGI  VYQ   L  +++V ENV+LG            +   AA 
Sbjct: 88  VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPARMRDEVAA- 146

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
             LA+    ++DP   +  +S+  +Q V I + +  +++VLILDEPT+ L   E   LF 
Sbjct: 147 --LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFE 204

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE-LIGMMIGKS 244
            M ++ D G A++F+SH L ++  + D + ILR G+ + E    D P    L   M+G+ 
Sbjct: 205 AMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRD 264

Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
              + Q+ AK+    +TP +  ++ V+ L   G ++ V + + +GE+V  AG+ G+G+ E
Sbjct: 265 V--VLQVDAKR----LTPVD-TVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKE 316

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
           L   + G  +P++G   + G+           +  +AY  E+R+       L +  N L+
Sbjct: 317 LVEAICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLL 376

Query: 365 AL--QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422
               Q  +G+F  + + EA   V + + E NV+P D   P + LSGGN QK++IGR    
Sbjct: 377 TTRNQFAKGVF--LDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFR 434

Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482
            PE+++ + PT+G+DI A  E+   +L+  S   GV+ ++ +L E + L+D I V+    
Sbjct: 435 KPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGR 493

Query: 483 KIAEIENDDTVSQATI 498
            I   + DDT     I
Sbjct: 494 FIDVFDKDDTAKVQAI 509



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 63/238 (26%), Positives = 117/238 (49%), Gaps = 10/238 (4%)

Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330
           K  GK    + + +DI  G +    G  G+G++ L  +L G  + D+GT  ++G     +
Sbjct: 37  KSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTVFA 96

Query: 331 DPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKK-EADAIVDKYM 389
            P  AL+  I    ++     ++  +TV +N+L+  Q+   + +P   + E  A+ ++Y 
Sbjct: 97  SPRDALRAGIGMVYQHFM---LVDSMTVAENVLLG-QSPDMLLRPARMRDEVAALAERYG 152

Query: 390 KELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVL 449
             +     DP   V  LS G +Q+V I + L     +LILDEPT  +      ++ + + 
Sbjct: 153 LAV-----DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMW 207

Query: 450 DLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNV 507
            +A QG  +VFIS +L+EV+ ++D+I +L+    + E    D  +Q  +   +   +V
Sbjct: 208 RMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV 265



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 52/234 (22%), Positives = 113/234 (48%), Gaps = 6/234 (2%)

Query: 13  ITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQ 72
           +++E      L  V L +  GE+ A+ G  G G+  +++A+ G+ +  AG + + G+P +
Sbjct: 281 LSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWR 340

Query: 73  FNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEKRGPFGIDWKKTH--EAAKKY 127
                     G+A + ++   +  C +L + +N +L    +   G+   +T    A K+ 
Sbjct: 341 EFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRV 400

Query: 128 LAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIM 187
           + +  ++  D   P  ++S    Q + I R      +V++ + PT  LD +   +++  +
Sbjct: 401 VWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRL 460

Query: 188 RKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
            + R +   +L V+  L++  E+ DR+ ++  G+FI      DT + + IG+M+
Sbjct: 461 LEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513


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: 663
Number of extensions: 31
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: 537
Length adjustment: 35
Effective length of query: 478
Effective length of database: 502
Effective search space:   239956
Effective search space used:   239956
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 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