Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate GFF5270 PS417_26985 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__WCS417:GFF5270 Length = 759 Score = 299 bits (765), Expect = 5e-85 Identities = 200/615 (32%), Positives = 323/615 (52%), Gaps = 31/615 (5%) Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQV- 294 E E + T++ LA A ++ E + + GV S G+A G V + Sbjct: 137 EGEEAFLVTMSAQLAGVIAHAEATGSIRGLGREGKGIQEAKFVGVPGSPGAAVGTAVVML 196 Query: 295 --AERTLEMPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQAD---IFKAHQELL 349 A+ + + +D E + + AL ++ L + A + + + +F +Q +L Sbjct: 197 PPADLDVVPDKTVSDIDAEIKLFKTALEGVRADMRNLSNKLATQLRPEERALFDVYQMML 256 Query: 350 EDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLI 409 +D SL + + +I G+ A A F+ + L ERA D+ D+G+R+L + Sbjct: 257 DDASLGNEVKTVIKTGQWAQGALRQVVTDHVNRFEMMDDDYLRERASDVRDLGRRLLAKL 316 Query: 410 LGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAV 469 PD IL++E+LT + + GK++G +V G SHVAILARA+G+P V Sbjct: 317 QEDRTTNLVYPDNTILVSEELTATMLGEVPEGKLVGLVSVLGSGNSHVAILARAMGIPTV 376 Query: 470 CGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARA-A 528 GL + G +++D +GE+ +P+ V+ + +A+ ++ ++ L++ Sbjct: 377 MGLVDLPYAKVDGIGMIVDGHRGEVFTNPS-EVLRKQYAEVVEEEKQLALGLDSLRELPC 435 Query: 529 VTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA 588 VT DGH + N LA+ +A GAEG+GL R+E + PS EQ Y Sbjct: 436 VTTDGHRVPLLVNTGLLADVARAQQRGAEGVGLYRTEVPFMINQRFPSEKEQLAIYREQL 495 Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAIL-S 647 +A P + +R+LD+GGDK L+Y P+ E NPFLG RGIR+ L+ P++ Q RA+L + Sbjct: 496 QAFHPLP-VTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTLDHPEIFLVQTRAMLKA 553 Query: 648 SAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE------------LPKLGIMIEV 695 S GL L I+LPM+S EL EEAL L R +P +G+MIE+ Sbjct: 554 SEGLNNLRILLPMISGTHEL--------EEALHLIHRAWGEVRDEGADVPMPPIGVMIEI 605 Query: 696 PAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAA 755 PAA A A +VDF S+G+NDLTQY LA+DR++PR+A D HP+VL+ + V+ A Sbjct: 606 PAAVYQAKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQALQHVVRDA 665 Query: 756 HAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQV 815 HA GK V +CG +A + A LL+ +G D LS++ +P +K +R+VELS + + ++ Sbjct: 666 HAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQVELSMAKDLLAEL 725 Query: 816 LGLESAEQVREALSV 830 + +++ + + +L + Sbjct: 726 MTIDNPQVIHSSLQL 740 Lambda K H 0.318 0.132 0.370 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: 1272 Number of extensions: 63 Number of successful extensions: 7 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: 844 Length of database: 759 Length adjustment: 41 Effective length of query: 803 Effective length of database: 718 Effective search space: 576554 Effective search space used: 576554 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: 55 (25.8 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