Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 206257 DVU0829 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >MicrobesOnline__882:206257 Length = 590 Score = 325 bits (833), Expect = 5e-93 Identities = 195/524 (37%), Positives = 294/524 (56%), Gaps = 23/524 (4%) Query: 319 ALQVLQDKAAGSAQ--------AEIFRAHQELLEDPTLL-EHAHRLLGEGKSAAFAWNSA 369 A QV D AQ A I +H+ + DP L+ + A R+ + SA +A A Sbjct: 51 AAQVASDLDRARAQVPADLRDHAAIIDSHRMICRDPKLMGDAARRIREQNISAPWALEQA 110 Query: 370 TLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQT 429 A F+ + + I ER D+ V +R+L + G ER +L+A LTP+ T Sbjct: 111 VDAIAQAFRAIDDPYIRERVQDVRAVAERILSRLAGNARELKSTGERMVLLAHDLTPADT 170 Query: 430 ASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELH 489 L +++ F T GG TSH ILAR+L +PA+ GV A A+G V++DA +G + Sbjct: 171 IELQVSRIMSFATAEGGKTSHTGILARSLQIPAVVGVSGLEEATADGDLVIIDALRGRIL 230 Query: 490 LEPN---LAEIEQLEAARKHQVLRHQRDVA-QASLPATTRDGHHVEVTANVASLQEVEHA 545 ++P+ LAE +L K+Q +QR + Q++LPA T DG+ +EV +N+ L+EV Sbjct: 231 IDPDEHELAEYTEL----KYQFESYQRSIRRQSTLPAETLDGYRIEVQSNIELLEEVPQV 286 Query: 546 LTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLA 605 L G +GVGL R+E+ +L R + PS ++ Y+ +A AL + R +V RTLDVG DK L Sbjct: 287 LDSGADGVGLYRTEYAFLARRQPPSEQDLCDEYSQVA-ALMSPRQVVFRTLDVGADKMLR 345 Query: 606 YVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELHLAR 665 E NP LGLR IR CL + R Q RAIL ++ + ++ PM+S + EL AR Sbjct: 346 EQVRMEEPNPALGLRAIRFCLRHQDVFRTQLRAILRASVHGNVALLFPMISGIQELRQAR 405 Query: 666 KILEE---EALALGLTELPKL--GIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAM 720 IL+E E A G+ P + GIM+E+PSA L+AD A VDFFSIGTNDL QY+L + Sbjct: 406 HILQEVRQELDAEGIPHAPDMPVGIMVELPSAVLIADALAHEVDFFSIGTNDLIQYSLGI 465 Query: 721 DRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDEL 780 DR + ++ HPA++R I V +AH G V VCG +AS+ +P+L+G+ +D + Sbjct: 466 DRGNRHVSYLYQPLHPAIVRSIKLVVDSAHRAGISVSVCGEVASDPFCLPILMGMQIDSI 525 Query: 781 SVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQ 824 S++ +P IK +R+ ++ +C+ + R VL + + +++ Sbjct: 526 SIAPQAVPGIKHIIRKTNMEECKTLTRDVLNATTVSTINRMVKE 569 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: 913 Number of extensions: 34 Number of successful extensions: 4 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: 590 Length adjustment: 39 Effective length of query: 799 Effective length of database: 551 Effective search space: 440249 Effective search space used: 440249 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: 54 (25.4 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