Alignments for a candidate for fruK in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Dinoroseobacter shibae DFL-12

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  296 bits (758), Expect = 1e-84
 Identities = 164/482 (34%), Positives = 284/482 (58%), Gaps = 13/482 (2%)

Query: 10  MKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGK 69
           ++ IT  + GV ALD VD T+ PGE   L GENG+GKST+IK ++GV    AG++ + G+
Sbjct: 12  LRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQ 71

Query: 70  PQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI-DWKKTHEAAKKYL 128
                    +  AG+  ++Q+ +L  NLSV EN+    +      +  ++   + A+  L
Sbjct: 72  EHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAAL 131

Query: 129 AQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMR 188
            ++G++ ID    + ++ +A +QLVAI RA+   A+++I+DEPT++L   EVR L  I+R
Sbjct: 132 DRIGVQ-IDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIR 190

Query: 189 KVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAEL 248
            +++ GVA++FVSH L ++ E+++++ +LRNG+ + E    +     L   M G+   E+
Sbjct: 191 MLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPEV 250

Query: 249 SQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRL 308
                     ++  G + ++ V+GLGK G+ + +  D+  GEV+G  GLLG GRT + + 
Sbjct: 251 PP-------SDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKA 303

Query: 309 LYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA-LQ 367
           L+G   PD+G+  ++G  V + DP  A   +I Y  E+R  EG+    ++ +N+ +  L 
Sbjct: 304 LFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLD 363

Query: 368 A-TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426
           A T G F  +     +A    +++ L V+  D + PV++LSGGNQQ+V + RWL+  P +
Sbjct: 364 AHTSGGFLDMTGLAKEA--SDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRV 421

Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486
           LIL+ P+ G+D+G+KA+I  ++ +LA +G+GV+ IS +L E++     + V+++   I  
Sbjct: 422 LILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDA 481

Query: 487 IE 488
           +E
Sbjct: 482 LE 483



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 60/216 (27%), Positives = 106/216 (49%), Gaps = 5/216 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           +   L  GEV  + G  G G++++ KAL G+   +AGSI+VDG P        A  A I 
Sbjct: 277 ISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIG 336

Query: 86  TVYQE---VNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKKYLAQMGLESIDPHT 140
            V ++     L  + S+  NV +G       G  +D     + A  +L ++ +++ D   
Sbjct: 337 YVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEA 396

Query: 141 PLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFV 200
           P+ S+S   QQ VA+AR +    +VLIL+ P+  +D     D+  I+R++   G+ ++ +
Sbjct: 397 PVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVI 456

Query: 201 SHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDEL 236
           S  L ++     R+ ++R G+ I  +       D+L
Sbjct: 457 SDDLPELLATCHRVLVMREGRIIDALEGTALTEDDL 492


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: 560
Number of extensions: 25
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 513
Length of database: 498
Length adjustment: 34
Effective length of query: 479
Effective length of database: 464
Effective search space:   222256
Effective search space used:   222256
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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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