GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Burk376:H281DRAFT_00426
          Length = 503

 Score =  353 bits (905), Expect = e-101
 Identities = 183/493 (37%), Positives = 313/493 (63%), Gaps = 10/493 (2%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ +K ++  FPGV+AL  V   L  GEVHALMGENGAGKST++K L GVY  ++G I+
Sbjct: 3   PLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEIL 62

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI--DWKKTHEA 123
           + G+P +     DAQ AGI  ++QE+ L  +L+V +N+ +G E RG  G+  D  K +  
Sbjct: 63  LGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNAK 122

Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183
           A++ L++M + +IDP   + ++++A QQ+V IA+A+  +++VLI+DEPTS+L+  E+ +L
Sbjct: 123 AREILSRMHV-NIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181

Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243
           F I+R+++  GV ++++SH +D++ +I DR+T+LR+G+++  V   DT  + +IGMM+G+
Sbjct: 182 FRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGR 241

Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
           + ++++  G   ++ EI       ++V+ L     +  V   + KGE++GFAGL+G+GRT
Sbjct: 242 TLSDVAPAGRAASQGEIA------LEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRT 295

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           E+ R ++GAD  +SG   + G K +I  P  A+ + I Y +E+R+  G+   + V  NI+
Sbjct: 296 EVARAVFGADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIV 355

Query: 364 IA-LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422
           ++ L+    +   + +         ++  L +R     + V+ LSGGNQQK++I +WL  
Sbjct: 356 MSNLRNFLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLER 415

Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482
             ++L  DEPTRGID+GAK+EI +++  LA +G  +V ISSEL E++R+SD + V+ +  
Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGR 475

Query: 483 KIAEIENDDTVSQ 495
              E+  +    +
Sbjct: 476 ITGELPAEQATQE 488



 Score =  102 bits (255), Expect = 2e-26
 Identities = 70/244 (28%), Positives = 126/244 (51%), Gaps = 8/244 (3%)

Query: 266 PIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           P++ VK L K       ++ V  D+ +GEV    G  G+G++ L ++L G    DSG   
Sbjct: 3   PLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEIL 62

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381
           L G+ V +  P  A    I    +  +   ++  LTV QNI I  +    +   + + + 
Sbjct: 63  LGGQPVELQSPRDAQAAGIGIIHQELQ---LMNHLTVAQNIFIGREPRGRLGLFLDEDKL 119

Query: 382 DAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAK 441
           +A   + +  ++V   DP   V NL+  +QQ V I + L+    +LI+DEPT  ++    
Sbjct: 120 NAKAREILSRMHVN-IDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEI 178

Query: 442 AEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVET 501
           AE+ +++ +L  +G+GVV+IS +++E+ +++D + VL+D   +A +   DT  +A I   
Sbjct: 179 AELFRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMM 238

Query: 502 IANT 505
           +  T
Sbjct: 239 VGRT 242



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 49/218 (22%), Positives = 101/218 (46%), Gaps = 6/218 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           V  TL  GE+    G  GAG++ + +A+ G   + +G I V G         DA   GI 
Sbjct: 274 VSFTLRKGEILGFAGLMGAGRTEVARAVFGADPVESGEIFVKGAKASIRTPSDAVAHGIG 333

Query: 86  TVYQE---VNLCTNLSVGENVMLGHEKRG---PFGIDWKKTHEAAKKYLAQMGLESIDPH 139
            + ++     L T + V  N+++ + +      F +   +    A  ++  + + +    
Sbjct: 334 YLSEDRKRFGLATGMDVESNIVMSNLRNFLSLNFFLRRARMRRRASHFINLLAIRTPSAA 393

Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199
             +  +S   QQ + IA+ +  +  VL  DEPT  +D     +++ ++R + D G AI+ 
Sbjct: 394 QQVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVM 453

Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           +S  L +I  ++DR+ ++  G+   E+  +   ++ ++
Sbjct: 454 ISSELPEILRMSDRVVVMCEGRITGELPAEQATQERIM 491


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: 571
Number of extensions: 26
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: 503
Length adjustment: 34
Effective length of query: 479
Effective length of database: 469
Effective search space:   224651
Effective search space used:   224651
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