Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 355 bits (910), Expect = e-102 Identities = 186/495 (37%), Positives = 311/495 (62%), Gaps = 15/495 (3%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ ++ + FPGV ALD L GEVHALMGENGAGKST++K L+GVY+ ++G I+ Sbjct: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEA 123 +DGKP + AQ GI ++QE+NL +LS +N+ +G E R G ID + + Sbjct: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183 A A+M L+ +DP TP+ +++A QQ+V IA+A+ +++VLI+DEPT++L+ E+ +L Sbjct: 141 AAAIFARMRLD-MDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243 F I+R ++ GV I+++SH +D++ +I DR++++R+G++I V ++T D +I MM+G+ Sbjct: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGR 259 Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 + +I +R ++ +++V+GL + I V + KGE++GFAGL+G+GRT Sbjct: 260 ALDGEQRIPPDTSRNDV------VLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRT 313 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 E+ R ++GAD ++G ++G K I P A+ + I Y +E+R+ G+ + V+ NI Sbjct: 314 EVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIA 373 Query: 364 IALQATRGMFKPIPKKEADAI---VDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWL 420 + ++ G F + + AI Y+++L ++ ++ + LSGGNQQK++I +WL Sbjct: 374 L---SSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430 Query: 421 ATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480 ++L DEPTRGID+GAK+EI +++ LA QG +V ISSEL EV+R+S + V+ + Sbjct: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490 Query: 481 RHKIAEIENDDTVSQ 495 E+ D + Sbjct: 491 GRITGELARADATQE 505 Score = 85.1 bits (209), Expect = 6e-21 Identities = 55/235 (23%), Positives = 113/235 (48%), Gaps = 7/235 (2%) Query: 21 KALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQ 80 +A+ V TL GE+ G GAG++ + +A+ G + AG I++ G DA Sbjct: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346 Query: 81 NAGIATVYQE---VNLCTNLSVGENVML---GHEKRGPFGIDWKKTHEAAKKYLAQMGLE 134 GI + ++ L + V N+ L G R F +D + EAA+ Y+ Q+ ++ Sbjct: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGF-MDQRAIREAAQMYVRQLAIK 405 Query: 135 SIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSG 194 + +S QQ + IA+ ++ + +L DEPT +D +++ ++ + + G Sbjct: 406 TPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQG 465 Query: 195 VAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELS 249 AI+ +S L ++ ++ R+ ++ G+ E+ D +++++ + + +A S Sbjct: 466 KAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESAVAS 520 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: 595 Number of extensions: 27 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 520 Length adjustment: 35 Effective length of query: 478 Effective length of database: 485 Effective search space: 231830 Effective search space used: 231830 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