Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 206413 DVU0981 multiphosphoryl transfer protein, putative
Query= TCDB::Q9HY55 (956 letters) >MicrobesOnline__882:206413 Length = 854 Score = 449 bits (1155), Expect = e-130 Identities = 331/844 (39%), Positives = 441/844 (52%), Gaps = 51/844 (6%) Query: 155 LGQNAEDLDELAWLGARLLKKAGCVENGF-------AAVLQQTEPLPLGDG---LCWLHS 204 LGQ +L E G L AG +++ V+ E + GDG L L S Sbjct: 13 LGQGLRELAEQMTQGRVPLAVAGGIDDPDHPIGTDPVRVMTAIEEVQQGDGVLVLMDLGS 72 Query: 205 EQLVKRPGLAFVTP---AQPLQHQGQLVTGLFC---LASLGEAHQALLERLCDLL----- 253 + L + P +Q LV GL LAS G A+ E L Sbjct: 73 ALMSAETALDLLPPEVASQVRLSAAPLVEGLMAAAVLASTGADLGAVAEEAQSALAAKRE 132 Query: 254 LEGRGAELVRATSSRSVLAALGGELP----PDWPSARAVLANPHGLHARPAQALAQLAKG 309 L G A A S A +P P V+ N GLHARPA + Sbjct: 133 LLGAAAPAAPAMPSAHPEGARDSTVPSSAMPAGEELTLVVPNRLGLHARPAARIVTALGP 192 Query: 310 FAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPALLAAVREGL 369 FA ++++ D VSA+S++++ L R G+T+ F A A AL A+ A Sbjct: 193 FAADVQLVRGDRV---VSARSVNRIATLAVRGGETVTFRAVGGDAALALRAIEALAAAHF 249 Query: 370 GEEVEALAEEALPDAV-----GEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQVAQR 424 G+ EA ++ P G+ E A A ++ G L+ AASPG+ G A V Sbjct: 250 GDAPEAPSKGEAPSPAEAPKDGDMAEAAVSADVQGGGVLRGAAASPGLTVGNA-VWYRPA 308 Query: 425 FE---FQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIR---EIFVTHREMLDDP 478 F+ P + PA E RL A A E+V L R+ A R EIF HR +LDD Sbjct: 309 FDAPDVAPLADDPATEVTRLDAALGAARTELVELERRTVAAAGRKEAEIFAMHRLLLDDV 368 Query: 479 ELAEQVQLRL-NRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCG 537 +A + R+ +R E+AE+AW V+ D+AA L + + ER AD+ D+G RVL L G Sbjct: 369 TIAGAARQRIMDRREAAESAWYEVISDAAATFRQLPEGYMREREADMVDVGARVLRLLTG 428 Query: 538 VEA--PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALV 595 V A PR P +L+ ++GPSD+A LD V GI+T +GGATSH+AI+AR+LGIPA+ Sbjct: 429 VAAVGPRLGG-PSVLLATDLGPSDMATLDPSLVIGIVTVQGGATSHAAILARSLGIPAVA 487 Query: 596 GAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPART 655 G G A+ G+ G + LDG G + V P+ A RDA + A A PA T Sbjct: 488 GLGPALQGVGEGDIVALDGGTGDVWVNPAPGVRAAVEARRDAWLAGREAALAGAAAPAVT 547 Query: 656 RDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDA 715 DG AV + AN+G +A A A++ GAEGVGL RTEF+F++ P Q Y A Sbjct: 548 ADGRAVHILANIGSSADAGAALKNGAEGVGLFRTEFLFLDRTSPPGEEEQLTAYVTAAAA 607 Query: 716 LDGRPLVARTLDVGGDKPLPYWP--IPHEENPYLGLRGIRLTLQRPQILETQLRALFRAA 773 + GRP+V RTLD+GGDKP+ Y E+NP+LGLRGIR L+R + TQLRAL RAA Sbjct: 608 MQGRPVVVRTLDIGGDKPVSYLEGFATGEDNPFLGLRGIRFCLERKPLFMTQLRALLRAA 667 Query: 774 GERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLADLQLGIMVEVPSAALLAPVL 828 PL+VMFPMV E A+ L R E +P L +GIM+EVP+A LA L Sbjct: 668 AVHPLKVMFPMVAHPGELAAAKALLDEARATLDAEGMPHGQLDVGIMIEVPAAVALADQL 727 Query: 829 AREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVC 888 AR+ FFS+GTNDL QY +A DRG+ S++A +D LHPAVL+++ TVRA HA G V +C Sbjct: 728 ARDAAFFSIGTNDLAQYVMAADRGNASVAALSDALHPAVLRMVRDTVRAGHAAGIPVAIC 787 Query: 889 GELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVR 948 GEL +P A+PLLVGL +DELS++ +I K VR LA +A+ L AA VR Sbjct: 788 GELGGNPEAIPLLVGLELDELSMNGPAIPRAKEVVRGCDTGTCAVLADRAMALPDAAAVR 847 Query: 949 ALVE 952 L++ Sbjct: 848 RLLQ 851 Lambda K H 0.318 0.134 0.382 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: 1717 Number of extensions: 78 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 956 Length of database: 854 Length adjustment: 43 Effective length of query: 913 Effective length of database: 811 Effective search space: 740443 Effective search space used: 740443 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 (21.7 bits) S2: 56 (26.2 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