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

GapMind for catabolism of small carbon sources

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

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  262 bits (669), Expect = 3e-74
 Identities = 161/493 (32%), Positives = 274/493 (55%), Gaps = 22/493 (4%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P + ++GI+  F  V+A   + + + PG +H ++GENGAGKST++  L G YK +AG I 
Sbjct: 24  PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           + G+  +   +  A  AGI  V+Q   L  N +V ENV+LG E+    G   + +   A+
Sbjct: 84  IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEE----GALLRPSLAKAR 139

Query: 126 KYLAQMGLE---SIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182
           K L ++  E   ++ P   +  +S+  QQ V I +A+   A +LILDEPT  L   E   
Sbjct: 140 KLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADH 199

Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242
           LF I+  ++  G  I+ ++H L +I E TD ++++R G+    V T DT  ++L  +M+G
Sbjct: 200 LFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVG 259

Query: 243 KSAA-ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301
           +     + +  A+     +T  +  +VD +G+ +   +  + + +  GEV+G AG+ G+G
Sbjct: 260 RKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVER---VKGISLQVRAGEVLGIAGVAGNG 316

Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNK----IAYSTENRRDEGIIGDLT 357
           ++EL  +L G  +P +G  T++G++++++  ++  K +    IA+  E+R+ EG+I D  
Sbjct: 317 QSELLEVL-GGMRPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYH 375

Query: 358 VRQNILIALQA----TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQK 413
             +N+           RG+        ADA  +  +   +VRPAD     KN SGGNQQK
Sbjct: 376 AWENVAFGYHDDPAYNRGLLMDNRAVRADA--EGKIARFDVRPADCWLAAKNFSGGNQQK 433

Query: 414 VLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSD 473
           +++ R +  +PELL++ +PTRG+DIGA   I Q ++ L   G  ++ +S ELEE++ LSD
Sbjct: 434 IVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSD 493

Query: 474 DIEVLKDRHKIAE 486
            + V+ D   + E
Sbjct: 494 RVAVMFDGRIMGE 506



 Score = 84.7 bits (208), Expect = 8e-21
 Identities = 59/235 (25%), Positives = 122/235 (51%), Gaps = 14/235 (5%)

Query: 264 EKPIVDVKGLGKK-GTINP---VDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGT 319
           + P ++++G+ K  G +     + + +  G + G  G  G+G++ L  +LYG  K D+G 
Sbjct: 22  QAPAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGE 81

Query: 320 YTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPK- 378
             + G+K  I D   A++  I    ++ +   ++ + TV +N+++  +    +   + K 
Sbjct: 82  IFIKGQKTEIPDSQAAIRAGIGMVFQHFK---LVENFTVLENVVLGAEEGALLRPSLAKA 138

Query: 379 -KEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437
            K    + ++Y  ELNV P   D  +++LS G+QQ+V I + L    ++LILDEPT  + 
Sbjct: 139 RKLLRELSEEY--ELNVAP---DALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLT 193

Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDT 492
                 + +++  L ++G  ++ I+ +L E++  +D + V++     A ++  DT
Sbjct: 194 PAEADHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADT 248



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 65/251 (25%), Positives = 119/251 (47%), Gaps = 17/251 (6%)

Query: 6   PIVVMKGI-TIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSI 64
           PI+ +  +  ++  GV+ + G+ L +  GEV  + G  G G+S +++ L G+ +   G +
Sbjct: 276 PILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSELLEVLGGM-RPATGRV 334

Query: 65  MVDGKPQQFNG------TLDAQNAGIATV---YQEVNLCTNLSVGENVMLGHEKRGPFG- 114
            V G+     G      T  AQ  GIA V    Q   L  +    ENV  G+     +  
Sbjct: 335 TVSGQQIDLTGKHSNGKTRRAQ--GIAHVPEDRQAEGLIMDYHAWENVAFGYHDDPAYNR 392

Query: 115 ---IDWKKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEP 171
              +D +     A+  +A+  +   D      + S   QQ + +AR +  N ++L++ +P
Sbjct: 393 GLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLAREIERNPELLLVGQP 452

Query: 172 TSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDT 231
           T  +D   +  +   +  +RD+G AIL VS  L++I  ++DR+ ++ +G+ + E    +T
Sbjct: 453 TRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMFDGRIMGERPAAET 512

Query: 232 PRDELIGMMIG 242
              EL  +M G
Sbjct: 513 NEKELGLLMAG 523


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: 708
Number of extensions: 41
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: 548
Length adjustment: 35
Effective length of query: 478
Effective length of database: 513
Effective search space:   245214
Effective search space used:   245214
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, or view the source code.

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