Alignments for a candidate for fruK in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Pseudomonas fluorescens FW300-N2C3

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  333 bits (855), Expect = 7e-96
 Identities = 181/494 (36%), Positives = 300/494 (60%), Gaps = 9/494 (1%)

Query: 3   DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62
           D+  ++ +  ++  FPGV AL  V L + PG V ALMGENGAGKST++K + G+Y+ +AG
Sbjct: 22  DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 81

Query: 63  SIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEK-RGPFGIDWKKTH 121
            + + GKP  F+  L A  AGIA ++QE+NL  ++S+ EN+ +G E+  G   +D  + H
Sbjct: 82  ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMH 141

Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181
               + L ++ ++ +DP   + ++SIA +Q+V IA+A+  ++ +LI+DEPTS++   EV 
Sbjct: 142 RCTARLLERLRIK-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVA 200

Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
            LF+I+  ++  G  I++++H +++++ I D + + R+G +I          D LI MM+
Sbjct: 201 HLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 260

Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301
           G+  ++L  +      RE   GE  ++ V+ L   G    V  D++ GE++G AGL+GSG
Sbjct: 261 GRELSQLFPV------REQPIGEL-VLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSG 313

Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361
           RT +   ++G      G   L+G+ V ISDP+ A++   A  TE+R+  G+   L+V +N
Sbjct: 314 RTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLEN 373

Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421
           + +A+         I +K   A+ +   K+L V+    ++ +  LSGGNQQK L+ RWL 
Sbjct: 374 MEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433

Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDR 481
           T+P +LILDEPTRGID+GAKAEI +++  LAS+GM V+ ISSEL EV+ +SD + V+ + 
Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEG 493

Query: 482 HKIAEIENDDTVSQ 495
             +  ++  +   +
Sbjct: 494 DLMGTLDRSEATQE 507



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 53/226 (23%), Positives = 111/226 (49%), Gaps = 7/226 (3%)

Query: 25  GVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGI 84
           GV   L+ GE+  + G  G+G++ + +A+ GV     G I +DG+P + +    A   G 
Sbjct: 293 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGF 352

Query: 85  ATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDP 138
           A + ++  L      LSV EN+   +L H     F I  K      +    ++ +++   
Sbjct: 353 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF-IQQKALRALCEDMCKKLRVKTPSL 411

Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198
              + ++S   QQ   +AR ++ N ++LILDEPT  +D     +++ ++  +   G+A++
Sbjct: 412 EQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVI 471

Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244
            +S  L ++  ++DR+ ++  G  +  +   +  ++ ++ +  G S
Sbjct: 472 MISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGLS 517


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: 634
Number of extensions: 29
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 478
Effective length of database: 482
Effective search space:   230396
Effective search space used:   230396
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