Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 243 bits (621), Expect = 1e-68 Identities = 162/496 (32%), Positives = 262/496 (52%), Gaps = 17/496 (3%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P+V + GI F V+A + L + PG + AL+GENGAGKST++ L G + +AG+I+ Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 VDG P F DA AGI VYQ L +++V ENV+LG + AA Sbjct: 88 VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPARMRDEVAA- 146 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 LA+ ++DP + +S+ +Q V I + + +++VLILDEPT+ L E LF Sbjct: 147 --LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFE 204 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE-LIGMMIGKS 244 M ++ D G A++F+SH L ++ + D + ILR G+ + E D P L M+G+ Sbjct: 205 AMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRD 264 Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304 + Q+ AK+ +TP + ++ V+ L G ++ V + + +GE+V AG+ G+G+ E Sbjct: 265 V--VLQVDAKR----LTPVD-TVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKE 316 Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364 L + G +P++G + G+ + +AY E+R+ L + N L+ Sbjct: 317 LVEAICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLL 376 Query: 365 AL--QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422 Q +G+F + + EA V + + E NV+P D P + LSGGN QK++IGR Sbjct: 377 TTRNQFAKGVF--LDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFR 434 Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482 PE+++ + PT+G+DI A E+ +L+ S GV+ ++ +L E + L+D I V+ Sbjct: 435 KPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGR 493 Query: 483 KIAEIENDDTVSQATI 498 I + DDT I Sbjct: 494 FIDVFDKDDTAKVQAI 509 Score = 85.5 bits (210), Expect = 4e-21 Identities = 63/238 (26%), Positives = 117/238 (49%), Gaps = 10/238 (4%) Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330 K GK + + +DI G + G G+G++ L +L G + D+GT ++G + Sbjct: 37 KSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTVFA 96 Query: 331 DPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKK-EADAIVDKYM 389 P AL+ I ++ ++ +TV +N+L+ Q+ + +P + E A+ ++Y Sbjct: 97 SPRDALRAGIGMVYQHFM---LVDSMTVAENVLLG-QSPDMLLRPARMRDEVAALAERYG 152 Query: 390 KELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVL 449 + DP V LS G +Q+V I + L +LILDEPT + ++ + + Sbjct: 153 LAV-----DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMW 207 Query: 450 DLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNV 507 +A QG +VFIS +L+EV+ ++D+I +L+ + E D +Q + + +V Sbjct: 208 RMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV 265 Score = 76.6 bits (187), Expect = 2e-18 Identities = 52/234 (22%), Positives = 113/234 (48%), Gaps = 6/234 (2%) Query: 13 ITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQ 72 +++E L V L + GE+ A+ G G G+ +++A+ G+ + AG + + G+P + Sbjct: 281 LSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWR 340 Query: 73 FNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEKRGPFGIDWKKTH--EAAKKY 127 G+A + ++ + C +L + +N +L + G+ +T A K+ Sbjct: 341 EFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRV 400 Query: 128 LAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIM 187 + + ++ D P ++S Q + I R +V++ + PT LD + +++ + Sbjct: 401 VWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRL 460 Query: 188 RKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 + R + +L V+ L++ E+ DR+ ++ G+FI DT + + IG+M+ Sbjct: 461 LEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513 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: 663 Number of extensions: 31 Number of successful extensions: 9 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: 537 Length adjustment: 35 Effective length of query: 478 Effective length of database: 502 Effective search space: 239956 Effective search space used: 239956 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