Alignments for a candidate for fruK in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Pseudomonas fluorescens FW300-N1B4

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  335 bits (859), Expect = 2e-96
 Identities = 187/484 (38%), Positives = 295/484 (60%), Gaps = 17/484 (3%)

Query: 17  FPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGT 76
           FPGV AL  V L + PG V ALMGENGAGKST++K + G+Y+ +AG + + GKP  F   
Sbjct: 42  FPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVVFETP 101

Query: 77  LDAQNAGIATVYQEVNLCTNLSVGENVMLGHEK-RGPFGIDWKKTHEAAKKYLAQMGLES 135
           L A  AGIA ++QE+NL  ++S+ EN+ +G E+  G   ID ++ H    K L ++ + +
Sbjct: 102 LAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTAKLLERLRI-N 160

Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195
           +DP   + ++SIA +Q+V IA+A+  ++ +LI+DEPTS++   EV  LF+I+  ++  G 
Sbjct: 161 LDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKRQGK 220

Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKK 255
            I++++H +++++ I D + + R+G +I          D LI MM+G+   ELSQ+   +
Sbjct: 221 GIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR---ELSQLFPVR 277

Query: 256 ARREITPGEKPIVD----VKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYG 311
                   EKPI D    V+ L   G    V  D++ GE++G AGL+GSGRT +   ++G
Sbjct: 278 --------EKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIFG 329

Query: 312 ADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRG 371
               D G   L+G+ V ISDP+ A++   A  TE+R+  G+   L+V +N+ +A+     
Sbjct: 330 ITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYV 389

Query: 372 MFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431
               I +K   A+ +   K+L V+    ++ +  LSGGNQQK L+ RWL T+P +LILDE
Sbjct: 390 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 449

Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491
           PTRGID+GAKAEI +++  LAS+GM V+ ISSEL EV+ +SD + V+ +   +  ++  +
Sbjct: 450 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 509

Query: 492 TVSQ 495
              +
Sbjct: 510 ATQE 513



 Score = 94.7 bits (234), Expect = 7e-24
 Identities = 63/225 (28%), Positives = 117/225 (52%), Gaps = 10/225 (4%)

Query: 261 TPGEKP----IVDV-KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKP 315
           TP ++P    I++V KG      ++ V + +  G V+   G  G+G++ L +++ G  +P
Sbjct: 25  TPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQP 84

Query: 316 DSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKP 375
           D+G   L GK V    P  AL+  IA      ++  ++  +++ +NI I  +   G+   
Sbjct: 85  DAGELRLRGKPVVFETPLAALQAGIAMI---HQELNLMPHMSIAENIWIGREQLNGLHM- 140

Query: 376 IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRG 435
           I  +E      K ++ L +   DP+  V NLS   +Q V I + ++   ++LI+DEPT  
Sbjct: 141 IDHREMHRCTAKLLERLRIN-LDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 199

Query: 436 IDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
           I     A +  ++ DL  QG G+++I+ ++ EV  ++D++ V +D
Sbjct: 200 ITDKEVAHLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRD 244



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 54/233 (23%), Positives = 114/233 (48%), Gaps = 11/233 (4%)

Query: 23  LDG----VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLD 78
           LDG    V   L+ GE+  + G  G+G++ + +A+ G+   + G I +DG+  + +    
Sbjct: 293 LDGIFKDVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHM 352

Query: 79  AQNAGIATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMG 132
           A   G A + ++  L      LSV EN+   +L H     F I  K      +    ++ 
Sbjct: 353 AIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF-IQQKALRALCEDMCKKLR 411

Query: 133 LESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192
           +++      + ++S   QQ   +AR ++ N ++LILDEPT  +D     +++ ++  +  
Sbjct: 412 VKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLAS 471

Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
            G+A++ +S  L ++  ++DR+ ++  G  +  +   +  ++ ++ +  G SA
Sbjct: 472 EGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSA 524


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: 638
Number of extensions: 29
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: 526
Length adjustment: 35
Effective length of query: 478
Effective length of database: 491
Effective search space:   234698
Effective search space used:   234698
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