GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Pseudomonas fluorescens GW456-L13

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  310 bits (795), Expect = 6e-89
 Identities = 177/473 (37%), Positives = 287/473 (60%), Gaps = 18/473 (3%)

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

Query: 72  QFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQM 131
            F  T D+  +G+A ++QE++L   ++V EN+ LGH     FG+  + T         + 
Sbjct: 80  DFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGH-LPASFGLINRSTLRQQALACLKG 138

Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191
             + IDP   +  +S+  +QLV IA+A+   A V+  DEPTSSL A E+  L AI+ ++R
Sbjct: 139 LADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLR 198

Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIK--EVMTKDTPRDELIGMMIGKSAAELS 249
           D G  +L+VSH +++++ I + +T+ ++G++++  + M++ T  D+L+  M+G+   ++ 
Sbjct: 199 DEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLT-HDQLVTCMVGRDIQDI- 256

Query: 250 QIGAKKARREITPGEKPIVDVK--GLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGR 307
                    +  P ++  V +K  GL   G   PV  +++KGE++G  GL+G+GRTEL R
Sbjct: 257 --------YDYRPRQRGAVALKVDGLLGPGLREPVSFEVHKGEILGLFGLVGAGRTELLR 308

Query: 308 LLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQ 367
           LL G  +  +G   L G ++ +  P  A+   I    E+R+ EGI+   +V +NI I+ +
Sbjct: 309 LLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISAR 368

Query: 368 ATRGMFKPIPKK--EADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPE 425
                F  + +   E D   ++ +K L V+  +  + +  LSGGNQQK ++GRWL+   +
Sbjct: 369 GAHSTFGCLLRGLWEKDN-AEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMK 427

Query: 426 LLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           +L+LDEPTRGIDIGAKAEI Q++ +LA++G+ V+ +SS+L EV+ +SD I VL
Sbjct: 428 VLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVL 480



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 56/238 (23%), Positives = 116/238 (48%), Gaps = 12/238 (5%)

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

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

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

Query: 190 VRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAE 247
           +   G+A++ VS  L ++  I+DR+ +L  G    E+  +      L+ + + +  A+
Sbjct: 453 LAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQLALPRQRAD 510



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 48/223 (21%), Positives = 105/223 (47%), Gaps = 10/223 (4%)

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

Query: 347 RRDEGIIGDLTVRQNILIA-LQATRGMF-KPIPKKEADAIVDKYMKELNVRPADPDRPVK 404
                ++ ++TV +N+ +  L A+ G+  +   +++A A +     E+     DP   V 
Sbjct: 99  LH---LVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGLADEI-----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   +   ++   ++   +V  +   ++
Sbjct: 211 MEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDI 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: 617
Number of extensions: 24
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.

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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:

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:

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:

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:

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