Alignments for a candidate for fruK in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Halomonas desiderata SP1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_002151265.1:WP_086510989.1
          Length = 497

 Score =  317 bits (812), Expect = 6e-91
 Identities = 176/479 (36%), Positives = 284/479 (59%), Gaps = 13/479 (2%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P +   GI++ FPGV+ALDGV    + G+VHALMGENGAGKST++K L+GV   + G++ 
Sbjct: 4   PYLRFDGISMVFPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGALW 63

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           +DG+   F    +A   GIA +YQE+ L  N++V EN++LG        I  ++  E A 
Sbjct: 64  IDGERHVFANAREALAQGIAIIYQELTLSPNMTVAENLLLGQLPTRHGFIKRRQLRERAL 123

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
             LA +G   I P T +  +SI  QQ++ I RA++ NA+++  DEPTSSL   E R L  
Sbjct: 124 AILADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLKR 183

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIK-EVMTKDTPRDELIGMMIGKS 244
           I+ ++R+ G  +L+V+H +++++++ D +T+ R+G+ I+          D L+  M+G+ 
Sbjct: 184 IISRLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGRD 243

Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
             ++         RE   GE  I+++  +  +G   PV  ++ +GEV G  GL+G+GR+E
Sbjct: 244 IEDV------YGYRERERGE-VILEIDAIEGRGLKAPVSFEVRRGEVFGLFGLVGAGRSE 296

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
           L RL+ GA++  +G     G+    + P  A++  IA   E+R+ +GI    +V  N+ I
Sbjct: 297 LMRLVCGAERASAGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNI 356

Query: 365 ALQ---ATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421
           + +      G+ +   ++ A+A  + Y++ L+++   P   +  LSGGNQQKV++ RWLA
Sbjct: 357 SCRRFFRRWGVLRDTRRERANA--EAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLA 414

Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
              EL ++DEPTRGID+GA+ +I  ++ DL  QG  VV ISS+L EV  + D I V++D
Sbjct: 415 EKIELFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRD 473



 Score = 93.6 bits (231), Expect = 1e-23
 Identities = 58/240 (24%), Positives = 125/240 (52%), Gaps = 8/240 (3%)

Query: 8   VVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVD 67
           V+++   IE  G+KA   V   +  GEV  L G  GAG+S +++ + G  + +AG +   
Sbjct: 258 VILEIDAIEGRGLKA--PVSFEVRRGEVFGLFGLVGAGRSELMRLVCGAERASAGEVRFQ 315

Query: 68  GKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEK---RGPFGIDWKKTH 121
           G+ ++F    +A   GIA   ++     +    SV +N+ +   +   R     D ++  
Sbjct: 316 GQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNISCRRFFRRWGVLRDTRRER 375

Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181
             A+ Y+ ++ +++  P T + ++S   QQ V +AR +    ++ ++DEPT  +D    R
Sbjct: 376 ANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWLAEKIELFVVDEPTRGIDVGARR 435

Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
           D++ ++  + + G +++ +S  L ++  I DR+ ++R+G  ++ V   +  ++ L+G+ +
Sbjct: 436 DIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRDGALVEVVPRHEATQERLLGLAL 495



 Score = 78.2 bits (191), Expect = 6e-19
 Identities = 54/223 (24%), Positives = 110/223 (49%), Gaps = 11/223 (4%)

Query: 279 INPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKN 338
           ++ V    + G+V    G  G+G++ L ++L G + P  G   ++G++   ++   AL  
Sbjct: 21  LDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGALWIDGERHVFANAREALAQ 80

Query: 339 KIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPAD 398
            IA   +      +  ++TV +N+L+    TR  F  I +++        + +L      
Sbjct: 81  GIAIIYQELT---LSPNMTVAENLLLGQLPTRHGF--IKRRQLRERALAILADLGEGDIH 135

Query: 399 PDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGV 458
           P   V+ LS G QQ + IGR L  +  ++  DEPT  + +    ++++++  L  +G  V
Sbjct: 136 PSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLKRIISRLREEGRVV 195

Query: 459 VFISSELEEVVRLSDDIEVLKD-RH-----KIAEIENDDTVSQ 495
           ++++  +EEV  + D + V +D +H      +A +++D  VS+
Sbjct: 196 LYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSE 238


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: 581
Number of extensions: 23
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: 513
Length of database: 497
Length adjustment: 34
Effective length of query: 479
Effective length of database: 463
Effective search space:   221777
Effective search space used:   221777
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 24 2021. The underlying query database was built on Sep 17 2021.

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