GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Pseudomonas fluorescens FW300-N2E3

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  337 bits (864), Expect = 6e-97
 Identities = 186/484 (38%), Positives = 296/484 (61%), Gaps = 17/484 (3%)

Query: 17  FPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGT 76
           FPGV AL  V L + PG V ALMGENGAGKST++K + G+Y+ +AG + + GKP  F+  
Sbjct: 37  FPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTP 96

Query: 77  LDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLAQMGLES 135
           L A  AGIA ++QE+NL  ++S+ EN+ +G E+   F  ID ++ H    + L ++ + +
Sbjct: 97  LAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERLRI-N 155

Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195
           +DP   + ++SIA +Q+V IA+A+  ++ +LI+DEPTS++   EV  LF+I+  ++  G 
Sbjct: 156 LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGK 215

Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKK 255
            I++++H +++++ I D + + R+G +I          D LI MM+G+   ELSQ+   +
Sbjct: 216 GIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR---ELSQLFPVR 272

Query: 256 ARREITPGEKPIVD----VKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYG 311
                   EKPI D    V+ L   G    V  D++ GE++G AGL+GSGRT +   ++G
Sbjct: 273 --------EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFG 324

Query: 312 ADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRG 371
               D G   L+G+ V ISDP+ A++   A  TE+R+  G+   L+V +N+ +A+     
Sbjct: 325 ITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA 384

Query: 372 MFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431
               I +K   A+ +   K+L V+    ++ +  LSGGNQQK L+ RWL T+P +LILDE
Sbjct: 385 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 444

Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491
           PTRGID+GAKAEI +++  LAS+GM V+ ISSEL EV+ +SD + V+ +   +  ++  +
Sbjct: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504

Query: 492 TVSQ 495
              +
Sbjct: 505 ATQE 508



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 65/242 (26%), Positives = 123/242 (50%), Gaps = 10/242 (4%)

Query: 244 SAAELSQIGAKKARREITPGEKP----IVDV-KGLGKKGTINPVDVDIYKGEVVGFAGLL 298
           ++A  S I     +    P ++P    I++V KG      ++ V + +  G V+   G  
Sbjct: 3   ASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGEN 62

Query: 299 GSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTV 358
           G+G++ L +++ G  +PD+G   L GK V    P  AL+  IA      ++  ++  +++
Sbjct: 63  GAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMI---HQELNLMPHMSI 119

Query: 359 RQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418
            +NI I  +   G F  I  +E      + ++ L +   DP+  V NLS   +Q V I +
Sbjct: 120 AENIWIGREQLNG-FHMIDHREMHRCTAQLLERLRIN-LDPEEQVGNLSIAERQMVEIAK 177

Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
            ++   ++LI+DEPT  I     A +  ++ DL +QG G+++I+ ++ EV  ++D++ V 
Sbjct: 178 AVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVF 237

Query: 479 KD 480
           +D
Sbjct: 238 RD 239



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 52/226 (23%), Positives = 112/226 (49%), Gaps = 7/226 (3%)

Query: 25  GVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGI 84
           GV   L+ GE+  + G  G+G++ + +A+ G+   + G I +DG+P + +    A   G 
Sbjct: 294 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGF 353

Query: 85  ATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDP 138
           A + ++  L      LSV EN+   +L H     F I  K      +    ++ +++   
Sbjct: 354 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGF-IQQKALRALCEDMCKKLRVKTPSL 412

Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198
              + ++S   QQ   +AR ++ N ++LILDEPT  +D     +++ ++  +   G+A++
Sbjct: 413 EQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVI 472

Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244
            +S  L ++  ++DR+ ++  G  +  +   +  ++ ++ +  G S
Sbjct: 473 MISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 518


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: 636
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: 521
Length adjustment: 35
Effective length of query: 478
Effective length of database: 486
Effective search space:   232308
Effective search space used:   232308
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