Alignments for a candidate for fruK in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Dyella japonica UNC79MFTsu3.2

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  298 bits (763), Expect = 3e-85
 Identities = 181/513 (35%), Positives = 281/513 (54%), Gaps = 18/513 (3%)

Query: 1   MTDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60
           M  ++ +  M+GI   F GVKALDG+DL L  GE   L GENGAGKST++K L+GVY   
Sbjct: 1   MAGESCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHG 60

Query: 61  A--GSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDW 117
           +  G I+  G+P +     D++ AGI  ++QE+ L   LSV EN+ LGHE   P G +D+
Sbjct: 61  SWDGEILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDY 120

Query: 118 KKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDA 177
              +  A   L ++GL  ++   P        QQL  IA+A+   AK+LILDEPTSSL +
Sbjct: 121 DAMYAKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTS 180

Query: 178 NEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           +E   L  I+  ++  GVA +++SH LD++  + D + ++R+G+ I      +   D LI
Sbjct: 181 SETEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLI 240

Query: 238 GMMIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINP-------VDVDIYKGE 290
            +M+G+    L        R E   GE  I + +       +NP       V   + +GE
Sbjct: 241 TLMVGRKLENLYP------RIEHAIGEV-IFEARHATCLDPVNPQRKRVDDVSFQLRRGE 293

Query: 291 VVGFAGLLGSGRTELGRLLYGADKPDSGTYT-LNGKKVNISDPYTALKNKIAYSTENRRD 349
           ++G AGL+G+GRTEL   ++GA    S     L G+ + I  P  A++  +    E+R+ 
Sbjct: 294 ILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKR 353

Query: 350 EGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGG 409
            GI+  L V  NI +A          I ++     ++  + E  V+ A P  P+  LSGG
Sbjct: 354 HGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGG 413

Query: 410 NQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVV 469
           NQQK ++ + L   P++LILDEPTRG+D+GAKAEI +++ +LA+QG+ +V +SSE+ EV+
Sbjct: 414 NQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVL 473

Query: 470 RLSDDIEVLKDRHKIAEIENDDTVSQATIVETI 502
            ++D + V+ +     +  N     +  +   I
Sbjct: 474 GMADRVLVMGEGRLRGDFPNQGLTQEQVLAAAI 506



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 58/234 (24%), Positives = 117/234 (50%), Gaps = 6/234 (2%)

Query: 18  PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG-SIMVDGKPQQFNGT 76
           P  K +D V   L  GE+  + G  GAG++ ++ A+ G Y   +   + ++G+P +    
Sbjct: 277 PQRKRVDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSP 336

Query: 77  LDAQNAGIATVYQEVN---LCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKKYLAQM 131
            DA  AG+  V ++     +   L VG+N+ L           ID ++   A +  +A+ 
Sbjct: 337 ADAIRAGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAER 396

Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191
            +++  P  P++ +S   QQ   +A+ ++   KVLILDEPT  +D     +++ ++ ++ 
Sbjct: 397 RVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELA 456

Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
             GVAI+ VS  + ++  + DR+ ++  G+   +   +   +++++   I  SA
Sbjct: 457 AQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQEQVLAAAIDTSA 510


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: 622
Number of extensions: 34
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: 513
Length adjustment: 35
Effective length of query: 478
Effective length of database: 478
Effective search space:   228484
Effective search space used:   228484
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