Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= TCDB::Q9HY55 (956 letters) >FitnessBrowser__Miya:8501869 Length = 846 Score = 447 bits (1151), Expect = e-129 Identities = 335/850 (39%), Positives = 444/850 (52%), Gaps = 73/850 (8%) Query: 155 LGQNAEDLDELAWLGARLLKKAGCVENGF-------AAVLQQTEPLPLGDG---LCWLHS 204 LGQ ++L E G L AG +++ V+ E + GDG L L S Sbjct: 13 LGQGVKELVEQMTQGRVPLAVAGGIDDPEHPIGTDPMRVMAAIEEVQQGDGVLVLMDLGS 72 Query: 205 EQLVKRPGLAFVTP---AQPLQHQGQLVTGLFCLASLGEAHQALLERLCDLLLEGRGAEL 261 + L + P AQ LV G+ A ++ L +L E + A Sbjct: 73 ALMSAETALDLLPPEVAAQVRLRPAPLVEGVMAAA----VQASIGADLDTVLREAQSALA 128 Query: 262 VRATSSRSVLAALGG---ELPPDWPSARAVLANPH----------GLHARPAQALAQLAK 308 +A L GG E P P+A A A H GLHARPA + Sbjct: 129 AKAELLGMALPQDGGGVDEAAP--PAAGATPAASHELTLMVPNRLGLHARPAARIVTALG 186 Query: 309 GFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPALLAAVREG 368 F + V+LA E VSA+S++++ L R G+T+ F A AE AL AL E Sbjct: 187 PFVAD--VQLARGERV-VSARSVNRIATLAVRGGETITFRAAGTDAEQALKALADLAAEN 243 Query: 369 LGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQA-----------IAASPGIASGPA 417 G+ LPDA + P GE+ +A + ASPGIA GPA Sbjct: 244 FGD---------LPDATKSSGRTGVEGPEGPGEQGRAGVAGVPAAKGGVPASPGIAVGPA 294 Query: 418 HVQVAQRFEFQP---RGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIR---EIFVTH 471 V F+ P P E RL A A +E+ L R+ A + EIFV H Sbjct: 295 -VWHRPAFDAPPPDLAAGDPDSEAARLDGALDAARKELAALERRTAAMAGKQEAEIFVMH 353 Query: 472 REMLDDPELAEQVQLRL-NRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRR 530 R +LDD +A + R+ R E AEAAW V++ +A L + + ERAADL D+G R Sbjct: 354 RLLLDDATIAGDARQRIAERREPAEAAWYAVIDQAAESFRQLPEGYMRERAADLVDVGAR 413 Query: 531 VLARLCGVEAPREP--EQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARA 588 VL L G P P E+P +L+ ++GPSD+A LD V GI+TA+GGATSH+AI+AR+ Sbjct: 414 VLRLLTGAP-PSGPRLERPSVLLAADLGPSDMAHLDPALVLGIVTAQGGATSHAAILARS 472 Query: 589 LGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQ 648 +GIPA+ GAGA + G + LDG G + +AP+ + L + R + + A A Sbjct: 473 MGIPAVAGAGALAASVADGVTVALDGSTGEVWIAPAPDVLSTIESRRASWLAVRQAALAG 532 Query: 649 RLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAE 708 PA T DG + V AN+G AA A++ GAEGVGL RTEF+F++ APD Q A Sbjct: 533 AARPAVTVDGRHMHVHANIGSPMDAAPALQNGAEGVGLFRTEFLFLDRVAAPDEEEQRAA 592 Query: 709 YRRVLDALDGRPLVARTLDVGGDKPLPYWP--IPHEENPYLGLRGIRLTLQRPQILETQL 766 Y A+ G P+V RTLD+GGDKP+PY EENP+LGLRGIR L R ++ TQL Sbjct: 593 YVAAAAAMPGLPVVVRTLDIGGDKPVPYLGDFAAGEENPFLGLRGIRFCLARRELFLTQL 652 Query: 767 RALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLADLQLGIMVEVPSA 821 RAL RAA E PLRVMFPMV E A+ L R + +P +++GIMVEVP+A Sbjct: 653 RALLRAAAEHPLRVMFPMVAHPGELAAAKALLEEARAALAAQGLPHGPVEVGIMVEVPAA 712 Query: 822 ALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAE 881 LA LARE FFS+GTNDL QY +A DRG+ +++ +D LHPAVL+++ TV A A Sbjct: 713 VALADQLARESAFFSIGTNDLAQYVMAADRGNAAVADLSDALHPAVLRMVRDTVAAGKAA 772 Query: 882 GKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGL 941 G V +CGELA + A+PLLVGLG+DELS++ +I K VR + A LA +AL L Sbjct: 773 GIPVAMCGELAGNADAIPLLVGLGLDELSMNGPAIPRAKDVVRGCDMTACVRLAGRALEL 832 Query: 942 ASAAEVRALV 951 AA VR L+ Sbjct: 833 PDAAAVRRLL 842 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: 1671 Number of extensions: 67 Number of successful extensions: 8 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: 846 Length adjustment: 43 Effective length of query: 913 Effective length of database: 803 Effective search space: 733139 Effective search space used: 733139 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 Apr 09 2024. 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