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.
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:
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