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_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  315 bits (806), Expect = 3e-90
 Identities = 180/471 (38%), Positives = 285/471 (60%), Gaps = 14/471 (2%)

Query: 12  GITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ 71
           GI   FPGVKALDG+    +PG+VHALMGENGAGKST++K L G Y  ++G + +  + +
Sbjct: 20  GIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIGEQKR 79

Query: 72  QFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQM 131
            F  T D+  +G+A ++QE++L   ++V EN+ LGH       I+     + A   L  +
Sbjct: 80  IFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALACLKGL 139

Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191
             + IDP   +  +S+  +QLV IA+A+   A V+  DEPTSSL A E+  L AI+ ++R
Sbjct: 140 A-DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLR 198

Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIK--EVMTKDTPRDELIGMMIGKSAAELS 249
           D G  +L+VSH +++++ I + +T+ ++G+F++  E M+  T  D+L+  M+G+   ++ 
Sbjct: 199 DEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALT-HDQLVTCMVGRDIQDIY 257

Query: 250 QIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLL 309
              ++       P     + V GL   G   PV  + +KGE++G  GL+G+GRTEL R+L
Sbjct: 258 DYRSR-------PRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRML 310

Query: 310 YGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQAT 369
            G  +  +G   L G+++ +  P  A+   I    E+R+ EGI+   +V +NI I+ +  
Sbjct: 311 SGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGA 370

Query: 370 RGMFKPIPKK--EADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELL 427
              F  + +   E D   DK +K L V+  +  + +  LSGGNQQK ++GRWL+   ++L
Sbjct: 371 HSTFGCLLRGLWEKDN-ADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVL 429

Query: 428 ILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           +LDEPTRGIDIGAKAEI Q++ +LA+ G+ V+ +SS+L EV+ +SD I VL
Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVL 480



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 57/232 (24%), Positives = 112/232 (48%), Gaps = 12/232 (5%)

Query: 18  PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTL 77
           PG++  + V    + GE+  L G  GAG++ + + L+G+ +  AG + + G+  + +   
Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPR 334

Query: 78  DAQNAGIATVYQE---VNLCTNLSVGENVMLGHE-KRGPFGID----WKKTHEAAKKYLA 129
           DA  AGI    ++     +    SV EN+ +        FG      W+K +  A K + 
Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDN--ADKQIK 392

Query: 130 QMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRK 189
            + +++ +    +  +S   QQ   + R + +  KVL+LDEPT  +D     +++ I+  
Sbjct: 393 ALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHN 452

Query: 190 VRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
           +  SG+A++ VS  L ++  I+DR+ +L  G    E+  +      L+ + +
Sbjct: 453 LAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLAL 504



 Score = 65.5 bits (158), Expect = 4e-15
 Identities = 50/223 (22%), Positives = 105/223 (47%), Gaps = 10/223 (4%)

Query: 287 YKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTEN 346
           + G+V    G  G+G++ L ++L GA  P SG   +  +K        ++ + +A   + 
Sbjct: 39  HPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIGEQKRIFKSTADSIGSGVAVIHQE 98

Query: 347 RRDEGIIGDLTVRQNILIA-LQATRGMF-KPIPKKEADAIVDKYMKELNVRPADPDRPVK 404
                ++ ++TV +N+ +  L A+ G+  + + +++A A +     E+     DP   V 
Sbjct: 99  LH---LVPEMTVAENLFLGHLPASFGLINRGVLRQQALACLKGLADEI-----DPQEKVG 150

Query: 405 NLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSE 464
            LS G +Q V I + L+    ++  DEPT  +       +  ++  L  +G  V+++S  
Sbjct: 151 RLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDEGKVVLYVSHR 210

Query: 465 LEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNV 507
           +EEV R+ + + V KD   +   E+   ++   +V  +   ++
Sbjct: 211 MEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDI 253


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: 610
Number of extensions: 27
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: 514
Length adjustment: 35
Effective length of query: 478
Effective length of database: 479
Effective search space:   228962
Effective search space used:   228962
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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