Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate H281DRAFT_01977 H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__Burk376:H281DRAFT_01977 Length = 854 Score = 601 bits (1549), Expect = e-176 Identities = 359/843 (42%), Positives = 510/843 (60%), Gaps = 30/843 (3%) Query: 9 LLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDSGHAVSITD 68 LLAP++G ++ L VPDPVFS + GDG+ +DP L AP G ++++ +GHAV++ Sbjct: 10 LLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCEGTVTHLARTGHAVTLAT 69 Query: 69 DNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARSLLTLMLVV 128 G ++L+HIG+DTV L G+GF ++++G V AG LIEFD D +AL+A SL++++ + Sbjct: 70 AEGAEILLHIGIDTVELNGKGFAPMIEQGAHVHAGDVLIEFDQDQIALHAPSLVSVIAIA 129 Query: 129 SGEPFSLLA---DGLVETGQ-PLLQLSP--SGAVEAVDEEEGDALFSKP---LTLPNANG 179 + + F ++ G+++ G+ PLL L P A +A + ++ + +TL +A G Sbjct: 130 NSDAFEIVERAQGGMLKAGETPLLLLRPRDGAAADASRQLSATSVTEEARAQVTLVHAGG 189 Query: 180 LHARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAA 239 LHARPAA +AA+GF+A + + + + A +S+V ++ L QG T+++ G A AA Sbjct: 190 LHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGQGATVELLGVGPQARAA 249 Query: 240 IKALV-ALLAEGCGEAVVNVA-------EPVATQSSATL----LRGVCASPGSAFGQVVQ 287 + A+ L E GE A + VA + TL L GVCASPG A G++V Sbjct: 250 VDAIADELTREAHGEVEEKPARQSSPAPQTVAPAAGETLAPNTLAGVCASPGVAIGKLVC 309 Query: 288 VTDPELVITEQGTG-GATERAALTRGLLAANEAL-QVLQDKAAGSA--QAEIFRAHQELL 343 D ++ EQ +G A E L + + + L ++D + A +A IF H+ LL Sbjct: 310 WDDADIDPPEQASGTSAAESRLLDKAIATVDTDLGTTVRDASQRGAVGEAGIFAVHRVLL 369 Query: 344 EDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLI 403 EDPTLL+ A L+ GKSA FAW A A + + + +AL+AERAADL D+ +RVL+ + Sbjct: 370 EDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRAL 429 Query: 404 LGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAI 463 +A LP+ A+L AE+ TPS ++LD +V V GGATSH AILAR G+PA+ Sbjct: 430 GYTNAAARALPDEAVLAAEEFTPSDLSALDRSRVTALVMARGGATSHAAILARQAGIPAL 489 Query: 464 CGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQ--LEAARKHQVLRHQRDVAQASLP 521 + + A+ G QV+++A G L P ++E+ LE +R V R +Q + Sbjct: 490 VAMGDALYAIPEGTQVVVNATTGRLEFAPTELDVERARLERSRLAGVREANRRTSQEA-- 547 Query: 522 ATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAI 581 A T DG +EV AN+A+L + + A+ G + VGLLR+E L++ R AP+ +E +Y I Sbjct: 548 AVTADGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQGI 607 Query: 582 ARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILA 641 AL + R ++RTLDVG DK + Y+ + E NP LGLRGIRL RP LL +Q R +L+ Sbjct: 608 VDAL-SGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLS 666 Query: 642 SAGFARLHIMLPMVSLLSELHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAP 701 F + I+LPMV+ + EL RK ++E A LG TE ++G+MIEVPSAAL+AD + Sbjct: 667 VKPFGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLSQ 726 Query: 702 HVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGA 761 H DF SIGTNDLTQYTLAMDR LA Q+D HPAVLRLIA TV+ A HGKWVGVCGA Sbjct: 727 HADFLSIGTNDLTQYTLAMDRCQADLAAQSDGLHPAVLRLIAATVQGASKHGKWVGVCGA 786 Query: 762 LASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREA 821 LA + LA+P+L+GLGV ELSV +P IKA VR LD C+ A+ L LE A VR Sbjct: 787 LAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAV 846 Query: 822 LRQ 824 R+ Sbjct: 847 SRE 849 Lambda K H 0.318 0.133 0.371 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: 1583 Number of extensions: 74 Number of successful extensions: 5 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: 838 Length of database: 854 Length adjustment: 42 Effective length of query: 796 Effective length of database: 812 Effective search space: 646352 Effective search space used: 646352 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