Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 326 bits (835), Expect = 1e-93 Identities = 171/475 (36%), Positives = 286/475 (60%), Gaps = 7/475 (1%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ + GI F GV AL V T+ PGEV AL+GENGAGKST++K LTG+++ + GSI Sbjct: 11 PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR--GPFGIDWKKTHEA 123 + G+ +F DA GI V+QE + LSV EN+ +G + P IDW++ + Sbjct: 71 LGGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRMEDE 130 Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183 A+ A++ ++ + + +S+A + V IARA+ A+V+I+DEPT++L +E+ +L Sbjct: 131 ARALFARLEVD-LPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGEL 189 Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243 + I+ ++R +G A++F+SH D+IY + DR T+LR+G+FI D +L+ +M+G+ Sbjct: 190 YRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGR 249 Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 ++ A + P +++VK L + V + GE++GF GL+G+GR+ Sbjct: 250 EVGQVFSRAASNTEDQTAP----VLEVKHLSHPSEFDDVSFAVRPGEILGFYGLVGAGRS 305 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 E+ L+G G ++G++V + P A+ + +AY E+R+ +G + L + QNI Sbjct: 306 EVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNIT 365 Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423 + + G F ++ I + ++L ++ + + V LSGGNQQKV++ +WLAT Sbjct: 366 LPVLPGIGFFLRRHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLATQ 425 Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478 P +LILDEPT+GIDIG+KA + + + +L +QG+ V+ +SSEL EV+ +SD I V+ Sbjct: 426 PRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVM 480 Score = 90.1 bits (222), Expect = 2e-22 Identities = 69/241 (28%), Positives = 120/241 (49%), Gaps = 16/241 (6%) Query: 266 PIVDVKGLGKK--GTINPVDVD--IYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321 P++ + G+GK+ G + DV + GEV+ G G+G++ L ++L G +PD G+ Sbjct: 11 PVLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIH 70 Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP---- 377 L G++V + A++ I T ++ + +L+V +NI I Q G + I Sbjct: 71 LGGREVRFASAQDAMRGGI---TAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRM 127 Query: 378 KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437 + EA A+ + +L VR VK+LS + V I R L+ +++I+DEPT + Sbjct: 128 EDEARALFARLEVDLPVRAR-----VKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALS 182 Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQAT 497 E+ +++ L G V+FIS + +E+ ++D VL+D IA E D Q Sbjct: 183 HHEIGELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQL 242 Query: 498 I 498 + Sbjct: 243 V 243 Score = 74.3 bits (181), Expect = 1e-17 Identities = 53/211 (25%), Positives = 104/211 (49%), Gaps = 6/211 (2%) Query: 24 DGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAG 83 D V + PGE+ G GAG+S ++ AL G+ G++ +DG+ + A G Sbjct: 282 DDVSFAVRPGEILGFYGLVGAGRSEVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHG 341 Query: 84 IATV---YQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA--AKKYLAQMGLESIDP 138 +A V Q +L + +N+ L F + + E A++ Q+ L++ Sbjct: 342 LAYVPEDRQRQGALLSLPIFQNITLPVLPGIGFFLRRHRRREIDIARRLCEQLELKASHF 401 Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198 H ++ +S QQ V +A+ + +VLILDEPT +D + + ++ G+A++ Sbjct: 402 HQHVAQLSGGNQQKVVLAKWLATQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVI 461 Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTK 229 VS L ++ ++DR+ ++ G+ +++V ++ Sbjct: 462 LVSSELPEVMGMSDRIVVMHQGR-VQQVFSR 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: 593 Number of extensions: 22 Number of successful extensions: 7 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: 505 Length adjustment: 34 Effective length of query: 479 Effective length of database: 471 Effective search space: 225609 Effective search space used: 225609 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