Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate Dsui_0742 Dsui_0742 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::azobra:AZOBR_RS32325 (846 letters) >FitnessBrowser__PS:Dsui_0742 Length = 579 Score = 296 bits (759), Expect = 2e-84 Identities = 198/577 (34%), Positives = 300/577 (51%), Gaps = 28/577 (4%) Query: 281 VPGIAASPGLAIGPVHVLPRAAVSVPDEPV-PLIEGGD--RLHEALSLTRQNLKALADDT 337 + G+ S G+AIG ++ A + V + P + + R A+ + L+ L + Sbjct: 5 IHGLGVSGGIAIGVAQLMSHATLEVAHLTIGPRMADKEVLRFEAAILAVQAELEQLKLEA 64 Query: 338 ARRLGPSEAAIFA-AQAEILNDTDLVTLACQLMVEGH-GVAWSWHQAVERTAAGLAALDN 395 ++ P+E F IL D +L + Q++ E W+ Q +ER A A+D+ Sbjct: 65 SKGNAPAELRAFVDLHGMILADPELSEVPKQIIRERRCNAEWAVVQQMERLVAQFDAIDD 124 Query: 396 PVLAARAADLRDVGQRVL-------ARIDPALRTGGAPDLPDTPCILIAEDLSPSDTAAL 448 L R AD+ V +RV+ R R GG T I++A DLSP+DT Sbjct: 125 AYLRERKADVVQVVERVVKVLMGHPGRSALRARKGGKET---TDQIIVAHDLSPADTIGF 181 Query: 449 DMARVIGLATAQGGPTSHTAILARTLGLPAMVAGGAALMELANGTPAILDGQSGRLHLSP 508 R T GG TSHTAILAR++ +P++V A + +G I+DG G + ++P Sbjct: 182 KEQRFASFITDVGGATSHTAILARSMAIPSIVGLHRARDLIRDGELLIIDGTRGVVIVNP 241 Query: 509 AAADIADARAWIAREEARKAEEEARRGLPARTRDGHEVEIGANVNRPDQVAVALSQGAES 568 + + R + E +++ + + + A T DG +V + AN+ P+ V A + GA+ Sbjct: 242 DERVLEEYRLRKSELELERSKLKRLKTMKATTLDGVDVLMYANIELPEDVEAARTAGADG 301 Query: 569 VGLMRTEFLFLERGDAPGEDEQYETYRGMLTALEGRPLIVRALDIGGDKQVPHLQLPHEE 628 +GL RTEFLFL RGD P EDEQ+E YR ++ +EG+P+ +R D+G DK + + + Sbjct: 302 IGLFRTEFLFLNRGDMPTEDEQFEAYRKVVKGMEGKPVTIRTFDLGADKALDAMDRV-KT 360 Query: 629 NPFLGVRGARLLLRRPELLETQLRALYRAAKDGGAKDGGALSIMFPMITALGEVQALRAA 688 NP LG+R RL L P++ TQLRA+ RA+K G K I+ PM+ E+ A AA Sbjct: 361 NPALGLRAIRLQLAEPKMFRTQLRAILRASKYGKVK------ILIPMLAHAHEIDATLAA 414 Query: 689 CERIRAELDA------PAVPLGIMVEVPAAAIQADVLARHVDFFSIGTNDLTQYALAIDR 742 + + L + +G M+E+PAAA+ + R +DF SIGTNDL QYALAIDR Sbjct: 415 VQAAKQSLREQKIGFDEGIEVGGMIEIPAAALAIGMFLRRLDFLSIGTNDLIQYALAIDR 474 Query: 743 QHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAGDPFGAALLTGLGVRELSM 802 ++ D LHPAVL L+ T+ E+ G V VCG +AGDP LL G+G+R SM Sbjct: 475 SDETVSQLYDPLHPAVLMLVAHTIYSGEKAGLPVSVCGELAGDPAMTRLLLGMGLRVFSM 534 Query: 803 TPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVR 839 P I VK + S+++ + ++ L + +R Sbjct: 535 HPSQILEVKQHVLKSEVAEIAPQVRKILRYSEPEKIR 571 Lambda K H 0.319 0.134 0.387 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: 1000 Number of extensions: 37 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: 846 Length of database: 579 Length adjustment: 39 Effective length of query: 807 Effective length of database: 540 Effective search space: 435780 Effective search space used: 435780 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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