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 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  373 bits (958), Expect = e-108
 Identities = 199/480 (41%), Positives = 302/480 (62%), Gaps = 9/480 (1%)

Query: 13  ITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQ 72
           IT  FPGVKAL  V L+LYPG+V AL+GENGAGKST++K LTG+Y+ + G I+VDG+P  
Sbjct: 26  ITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVP 85

Query: 73  FNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLAQM 131
           F+    A + G+  ++QE  L   LSV EN+ LGH  RG FG IDWKKT E A+  L  +
Sbjct: 86  FSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARALLTSI 145

Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191
           G E +DP   L  + IA + LVAIARA+ I A+V+I+DEPT++L   E+ +L+ ++  ++
Sbjct: 146 GAE-LDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLK 204

Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQI 251
             G AILF+SH  D+I+ I D  T+ R+GQ I +    D    +L+ MM+G+   ++SQI
Sbjct: 205 AQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGR---DVSQI 261

Query: 252 GAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYG 311
             ++A          ++ V+G       + +   + +GE++GF GL+G+GR+E  + L+G
Sbjct: 262 FPQRAPNV----GDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFG 317

Query: 312 ADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRG 371
             +P +G+  + G +  IS P  A+ + I Y  E+R  +G I DL + QN+ +       
Sbjct: 318 ITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRIS 377

Query: 372 MFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431
               +   E  A+  +Y + L++R A  D  V NLSGGNQQKV+I +WLAT P ++ILDE
Sbjct: 378 RKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDE 437

Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491
           PT+G+DIG+KA +   + +LA+QG+ V+ +SSE+ EV+ +SD + V+++   +AE+  DD
Sbjct: 438 PTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDD 497



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 58/220 (26%), Positives = 111/220 (50%), Gaps = 7/220 (3%)

Query: 24  DGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAG 83
           D +  TL  GE+    G  GAG+S  +++L G+ + +AGS+ + G   + +   DA + G
Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345

Query: 84  IATVYQE---VNLCTNLSVGENVML---GHEKRGPFGIDWKKTHEAAKKYLAQMGLESID 137
           I  V ++        +L + +NV L   G   R  F +   +    A++Y  ++ L +  
Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGF-LRLAEEFALAREYTERLDLRAAS 404

Query: 138 PHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAI 197
             T + ++S   QQ V IA+ +    +V+ILDEPT  +D      +   M ++   G+A+
Sbjct: 405 LDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAV 464

Query: 198 LFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           + VS  + ++  ++DR+ ++R G+ + E+   D   + L+
Sbjct: 465 IMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLV 504


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: 655
Number of extensions: 28
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: 510
Length adjustment: 35
Effective length of query: 478
Effective length of database: 475
Effective search space:   227050
Effective search space used:   227050
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