Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf6N2E2_3942 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3942 Length = 759 Score = 299 bits (765), Expect = 5e-85 Identities = 205/617 (33%), Positives = 319/617 (51%), Gaps = 35/617 (5%) Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGY-VVQV 294 E E + T++ LA A ++ + + + GV S G+A G VV + Sbjct: 137 EGEEAFLVTMSAQLAGVIAHAEATGSISGLGRQGKGIQEAKFVGVPGSPGAAVGTAVVML 196 Query: 295 AERTLEM------PEFAADQQLERESLE--RALMHATQALQRLRDNAAGEAQADIFKAHQ 346 L++ + A+ L + ++E RA M A A +L E +A +F + Sbjct: 197 PPADLDVVPDKAITDIDAELGLFKTAIEGVRADMRALSA--KLATQLRPEERA-LFDVYL 253 Query: 347 ELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVL 406 +L+D SL + +I G+ A A F+ + L ERA D+ D+G+R+L Sbjct: 254 MMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLRERASDVKDLGRRLL 313 Query: 407 KLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGL 466 + PD IL++E+LTP+ + GK+ G +V G SHVAILARA+G+ Sbjct: 314 AYLQQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAGLVSVLGSGNSHVAILARAMGI 373 Query: 467 PAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAAR 526 P V GL S G ++++D GE++ +P+ + +Q ++++Q Sbjct: 374 PTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVEEEKQLSLGLDALRDL 433 Query: 527 AAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSA 586 VT DGH + N LA+ +A GAEG+GL R+E + PS EQ Y Sbjct: 434 PCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQRFPSEKEQLAIYRE 493 Query: 587 IARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAIL 646 A PQ + +R+LD+GGDK L+Y P+ E NPFLG RGIR+ L+ P++ Q RA+L Sbjct: 494 QLAAFHPQP-VTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTLDHPEIFLVQARAML 551 Query: 647 -SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE------------LPKLGIMI 693 +S GL L I+LPM+S EL EEAL L R +P +G+MI Sbjct: 552 KASEGLNNLRILLPMISGTHEL--------EEALHLIHRAWGEVRDEGTDVPMPPIGVMI 603 Query: 694 EVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVK 753 E+PAA A +VDF S+G+NDLTQY LA+DR++PR+A D HP+VL+ + + V+ Sbjct: 604 EIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQALQNVVR 663 Query: 754 AAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAH 813 AHA GK V +CG +A + A LL+ +G D LS++ +P +K +R++ LS Q + Sbjct: 664 DAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSKAQELLA 723 Query: 814 QVLGLESAEQVREALSV 830 +V+ +++ + + +L + Sbjct: 724 EVMTIDNPQVIHSSLQL 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: 1268 Number of extensions: 58 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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