Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 385 bits (990), Expect = e-111 Identities = 209/490 (42%), Positives = 321/490 (65%), Gaps = 15/490 (3%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 I+ +KG++ FPGV ALDG+DL L GEVHA+ GENGAGKST++K ++G Y+ + G + Sbjct: 23 ILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRY 82 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHE-KRGPFGIDWKKTHEAAK 125 G P QF+ T DAQ AGIA ++QE+NL +LSV EN+ L E KRGPF +D++ + A+ Sbjct: 83 RGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPF-VDYRTLNSNAQ 141 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 + L ++GL ++ P T + ++S+A QQ+V IA+A+ ++A+VLI+DEPTSSL +E LF Sbjct: 142 RCLQRIGL-NVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFR 200 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 I+R++R GVAIL++SH LD++ EI DR+T+LR+G+ I T +E++ M+G+ Sbjct: 201 IIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVNEIVARMVGR-- 258 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 + R+ TP + ++ V+ L + G P+ ++ KGE++GFAGL+G+GRTE Sbjct: 259 ----PLDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTET 314 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365 R ++GA++PDSG+ TL + V I P A+++ IAY +E+R+ +G+ + V NI +A Sbjct: 315 ARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLA 374 Query: 366 ---LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422 ++RG + E AI ++Y++EL +R + +NLSGGNQQK++I +WL Sbjct: 375 NVRAISSRGFLR---FSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYR 431 Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482 +L DEPTRGID+GAK I ++ LA+ G+GVV ISSEL E++ ++D I V + Sbjct: 432 GSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGR 491 Query: 483 KIAEIENDDT 492 A +E T Sbjct: 492 ITAVLETRQT 501 Score = 80.1 bits (196), Expect = 2e-19 Identities = 51/224 (22%), Positives = 111/224 (49%), Gaps = 9/224 (4%) Query: 30 LYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIATVYQ 89 L GE+ G GAG++ +A+ G + ++GSI + +P +A GIA + + Sbjct: 295 LRKGEILGFAGLMGAGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSE 354 Query: 90 EVN---LCTNLSVGENVMLGHEK----RGPFGIDWKKTHEAAKKYLAQMGLESIDPHTPL 142 + L ++ V N+ L + + RG + + + A++Y+ ++G+ + Sbjct: 355 DRKKDGLALSMPVSANITLANVRAISSRG--FLRFSEETAIAERYVRELGIRTPTVKQIA 412 Query: 143 SSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVSH 202 ++S QQ + I++ + +++L DEPT +D ++ +M ++ GV ++ +S Sbjct: 413 RNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISS 472 Query: 203 FLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246 L ++ +TDR+ + G+ + T+ T ++E++ G+S A Sbjct: 473 ELPELLGMTDRIAVFHEGRITAVLETRQTSQEEILHHASGRSHA 516 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: 607 Number of extensions: 22 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: 516 Length adjustment: 35 Effective length of query: 478 Effective length of database: 481 Effective search space: 229918 Effective search space used: 229918 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