Alignments for a candidate for fruK in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Phyllobacterium brassicacearum STM 196

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_106714515.1 CU102_RS28785 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_003010955.1:WP_106714515.1
          Length = 513

 Score =  347 bits (890), Expect = e-100
 Identities = 188/472 (39%), Positives = 298/472 (63%), Gaps = 10/472 (2%)

Query: 11  KGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKP 70
           + I  EFPGV ALD V   L  G VHALMGENGAGKST++K L G+Y  + G + + G P
Sbjct: 27  ENIRKEFPGVLALDNVQFRLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGEVYLKGLP 86

Query: 71  QQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLA 129
            +    LDA   GIA ++QE+NL   ++V EN+ +  E +  FG +D  K ++       
Sbjct: 87  IRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNGFGFVDHGKMYDMTADLFK 146

Query: 130 QMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRK 189
           ++ + ++DP + +  +S+A +Q+V IA+A+   + VLI+DEPTS+L   EV  LF I+R 
Sbjct: 147 RLNI-TLDPESQVRDLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVEHLFQIIRD 205

Query: 190 VRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELS 249
           +R+ G+ I++++H +++++EI D  ++ R+G++I    + D  RD++I MM+G+   E++
Sbjct: 206 LREQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIKMMVGR---EIT 262

Query: 250 QIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLL 309
           Q+  K    EI P    ++ VK L  K   + V  D+  GE++G AGL+GSGR+ +   +
Sbjct: 263 QMFPK----EIVPIGDVVLSVKDLSLKNVFHDVSFDVRAGEILGVAGLVGSGRSNVAETI 318

Query: 310 YGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQAT 369
           +G     SGT T+ G+ + ++ P  A+ + +A+ TE+R++ G +  L V +N+ IA+   
Sbjct: 319 FGVTPATSGTITIKGQPIKMNSPTQAISHGMAFITEDRKETGCLLILDVLENMQIAVLQD 378

Query: 370 RGMFKPIPKKEADAIVDKYMKE-LNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLI 428
           R +     +++  A   K M + L V+    +  V+NLSGGNQQKVLIGRWL T+P++LI
Sbjct: 379 RFVKYGFVEEKQIAKACKAMSDTLRVKTPSLEETVENLSGGNQQKVLIGRWLLTNPKILI 438

Query: 429 LDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
           LDEPTRGID+GAKAEI +++  LA  G+ V+ ISSE+ EV+ +SD I V+ +
Sbjct: 439 LDEPTRGIDVGAKAEIHRLISQLAKTGVAVIMISSEMPEVLGMSDRIMVMHE 490



 Score = 94.0 bits (232), Expect = 1e-23
 Identities = 62/220 (28%), Positives = 111/220 (50%), Gaps = 10/220 (4%)

Query: 279 INPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKN 338
           ++ V   + +G V    G  G+G++ L ++L G   PD G   L G  + +  P  AL+N
Sbjct: 39  LDNVQFRLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGEVYLKGLPIRLKSPLDALEN 98

Query: 339 KIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPAD 398
            IA      ++  ++  +TV +NI I  +   G       K  D   D + K LN+   D
Sbjct: 99  GIAMI---HQELNLMPFMTVAENIWIRREPKNGFGFVDHGKMYDMTADLF-KRLNIT-LD 153

Query: 399 PDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGV 458
           P+  V++LS  N+Q V I + ++   ++LI+DEPT  +       + Q++ DL  QG+G+
Sbjct: 154 PESQVRDLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVEHLFQIIRDLREQGIGI 213

Query: 459 VFISSELEEVVRLSDDIEVLKD-----RHKIAEIENDDTV 493
           V+I+ ++ E+  ++D+  V +D      H   ++  DD +
Sbjct: 214 VYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDII 253



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 49/202 (24%), Positives = 105/202 (51%), Gaps = 6/202 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           V   +  GE+  + G  G+G+S + + + GV    +G+I + G+P + N    A + G+A
Sbjct: 291 VSFDVRAGEILGVAGLVGSGRSNVAETIFGVTPATSGTITIKGQPIKMNSPTQAISHGMA 350

Query: 86  TVYQ---EVNLCTNLSVGENVMLG--HEKRGPFG-IDWKKTHEAAKKYLAQMGLESIDPH 139
            + +   E      L V EN+ +    ++   +G ++ K+  +A K     + +++    
Sbjct: 351 FITEDRKETGCLLILDVLENMQIAVLQDRFVKYGFVEEKQIAKACKAMSDTLRVKTPSLE 410

Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199
             + ++S   QQ V I R ++ N K+LILDEPT  +D     ++  ++ ++  +GVA++ 
Sbjct: 411 ETVENLSGGNQQKVLIGRWLLTNPKILILDEPTRGIDVGAKAEIHRLISQLAKTGVAVIM 470

Query: 200 VSHFLDQIYEITDRLTILRNGQ 221
           +S  + ++  ++DR+ ++  G+
Sbjct: 471 ISSEMPEVLGMSDRIMVMHEGR 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: 631
Number of extensions: 31
Number of successful extensions: 8
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: 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 24 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 2024 update 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