Alignments for a candidate for fruK in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Pseudomonas simiae WCS417

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  340 bits (872), Expect = 7e-98
 Identities = 185/480 (38%), Positives = 296/480 (61%), Gaps = 9/480 (1%)

Query: 17  FPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGT 76
           FPGV AL  V L + PG V ALMGENGAGKST++K + G+Y+ +AG I + GKP  F   
Sbjct: 33  FPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETP 92

Query: 77  LDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLAQMGLES 135
           L AQ AGIA ++QE+NL  ++S+ EN+ +G E+      ++ ++ H    + LA++ + +
Sbjct: 93  LAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRI-N 151

Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195
           +DP   + ++SIA +Q+V IA+A+  ++ +LI+DEPTS++   EV  LF+I+  ++  G 
Sbjct: 152 LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGK 211

Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKK 255
            I++++H +++++ I D + + R+G +I          D LI MM+G+  ++L  +    
Sbjct: 212 GIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFPL---- 267

Query: 256 ARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKP 315
             RE TP    ++ V+ L   G    V  D++ GE++G AGL+GSGRT +   ++G    
Sbjct: 268 --RE-TPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPS 324

Query: 316 DSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKP 375
            SG  TL+GK V ISDP+ A++   A  TE+R+  G+   L+V +N+ +A+         
Sbjct: 325 SSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGF 384

Query: 376 IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRG 435
           I +K   A+ +   K+L V+    ++ +  LSGGNQQK L+ RWL T+P LLILDEPTRG
Sbjct: 385 IQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRG 444

Query: 436 IDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQ 495
           ID+GAKAEI +++  LAS+GM V+ ISSEL EV+ +SD + V+ +   +  ++  +   +
Sbjct: 445 IDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQE 504



 Score = 92.8 bits (229), Expect = 3e-23
 Identities = 59/238 (24%), Positives = 119/238 (50%), Gaps = 6/238 (2%)

Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330
           KG      +  V + +  G V+   G  G+G++ L +++ G  +PD+G   L GK +   
Sbjct: 31  KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90

Query: 331 DPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMK 390
            P  A K  IA      ++  ++  +++ +NI I  +    +   +  +E      + + 
Sbjct: 91  TPLAAQKAGIAMI---HQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCTAELLA 146

Query: 391 ELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLD 450
            L +   DP+  V NLS   +Q V I + ++   ++LI+DEPT  I     A +  ++ D
Sbjct: 147 RLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIAD 205

Query: 451 LASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNVN 508
           L SQG G+V+I+ ++ EV  ++D++ V +D H I  ++  D+++  +++  +    ++
Sbjct: 206 LKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 53/233 (22%), Positives = 116/233 (49%), Gaps = 11/233 (4%)

Query: 23  LDGV----DLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLD 78
           LDGV       L+ GE+  + G  G+G++ + + + G+   ++G I +DGK  + +    
Sbjct: 284 LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHM 343

Query: 79  AQNAGIATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMG 132
           A   G A + ++  L      LSV EN+   +L H     F I  K      +    ++ 
Sbjct: 344 AIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGF-IQQKALRALCEDMCKKLR 402

Query: 133 LESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192
           +++      + ++S   QQ   +AR ++ N ++LILDEPT  +D     +++ ++  +  
Sbjct: 403 VKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLAS 462

Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
            G+A++ +S  L ++  ++DR+ ++  G+ +  +   +  +++++ +  G +A
Sbjct: 463 EGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASGMTA 515


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: 623
Number of extensions: 28
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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