Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_2284 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2284 Length = 759 Score = 296 bits (759), Expect = 2e-84 Identities = 197/576 (34%), Positives = 307/576 (53%), Gaps = 39/576 (6%) Query: 279 GVCASAGSAFGYVVQ---------VAERTLEMPEFAADQQLERESLE--RALMHATQALQ 327 GV S G+A G V V ++T+ + A+ L + ++E RA M A A Sbjct: 180 GVPGSPGAAVGTAVVMLPPADLDVVPDKTIT--DINAELGLFKTAIEGVRADMRALSA-- 235 Query: 328 RLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLG 387 +L E +A +F + +L+D SL + +I G+ A A F+ + Sbjct: 236 KLATQLRPEERA-LFDVYLMMLDDASLGSEITTVIKTGQWAQGALRQVVTEHVNRFELMD 294 Query: 388 STLLAERALDLMDVGQRVLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFA 447 L ERA D+ D+G+R+L + PD IL++E+LTP+ + GK++G Sbjct: 295 DAYLRERASDVKDLGRRLLAYLQEERQQTLVYPDNTILVSEELTPAMLGEVPEGKLVGLV 354 Query: 448 TVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLH 507 +V G SHVAILARA+G+P V GL S G ++++D GE++ +P+ + +Q Sbjct: 355 SVLGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFA 414 Query: 508 AKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFL 567 ++++Q VT DGH + N LA+ +A GAEG+GL R+E Sbjct: 415 EVVEEEKQLALGLDALRDLPCVTVDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVP 474 Query: 568 YQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRG 627 + PS EQ Y A PQ + +R+LD+GGDK L+Y P+ E NPFLG RG Sbjct: 475 FMINQRFPSEKEQLAIYREQLAAFHPQP-VTMRSLDIGGDKALSYFPI-KEDNPFLGWRG 532 Query: 628 IRLCLERPQLLREQFRAIL-SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE- 685 IR+ L+ P++ Q RA+L +S GL L I+LPM+S + EL EEAL L R Sbjct: 533 IRVTLDHPEIFLVQTRAMLKASEGLNNLRILLPMISGIHEL--------EEALHLIHRAW 584 Query: 686 -----------LPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLA 734 +P +G+MIE+PAA A +VDF S+G+NDLTQY LA+DR++PR+A Sbjct: 585 GEVRDEGTDVPMPPVGVMIEIPAAVYQTRELARQVDFLSVGSNDLTQYLLAVDRNNPRVA 644 Query: 735 SQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIP 794 D HP+VL+ + + V+ AHA GK V +CG +A + A LL+ +G D LS++ +P Sbjct: 645 DLYDYLHPAVLQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLP 704 Query: 795 AIKAAIREVELSDCQAIAHQVLGLESAEQVREALSV 830 +K +R++ LS + + +++ +++ + + +L + Sbjct: 705 KVKWMLRQINLSKAKELLAELMTIDNPQVIHSSLQL 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: 1244 Number of extensions: 59 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