GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00426 H281DRAFT_00426
           monosaccharide ABC transporter ATP-binding protein, CUT2
           family
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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