Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 5208528 Shew_1039 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__PV4:5208528 Length = 743 Score = 317 bits (812), Expect = 2e-90 Identities = 217/627 (34%), Positives = 324/627 (51%), Gaps = 22/627 (3%) Query: 211 KSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSATL 270 K ++ ++ +Q Q D Q S A EA + L A LA E V + + Sbjct: 117 KLILGVLVVQ--QADARQFSEA---EEAFLMTLAAQLAVAVREQ--RKKAEVKSAPDKCV 169 Query: 271 LRGVCASPGSAFGQVVQVTDPELVITEQGTGGAT---ERAALTRGLLAANEALQVLQDKA 327 G A+ G + V E+ + +QG E AL++ L A L L + Sbjct: 170 YTGTSAASGVVIAHAM-VLGGEIPLEQQGRRTKQVDEELLALSQALDACRNTLSALSQRF 228 Query: 328 AGSAQAE---IFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLGNAL 384 G + E IF A Q LL+D +L R + G +A A + +L + FQ + + Sbjct: 229 DGENEKEVQSIFSALQLLLDDTSLGGEYGREIQAGWTAISAVSRVSLRYIDHFQQMQDPY 288 Query: 385 IAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVTVA 444 + ERA D+ D+GQRVL+ ++ Q +L IL+ ++ T + A K++G VT Sbjct: 289 MQERATDIRDLGQRVLRELIEPQKMQLELDVPVILVTKEATATMLAEFPQHKLVGIVTEL 348 Query: 445 GGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEAAR 504 GG SH AILARA G+PA+ GV + A +GKQ++L+A++G++ + P I + + Sbjct: 349 GGVNSHAAILARAFGVPAVIGVEGILNAGIDGKQLILNANRGQVLISPTPTLIGEYRSLI 408 Query: 505 KHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFLYLD 564 + +R + S PA T D + + N L + + G +GVGL R+E ++ Sbjct: 409 SAEKALQKRYAEELSKPAMTLDERRIHLYLNAGLLSSLASEIAEGADGVGLYRTEIPFML 468 Query: 565 RNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRGIRL 624 + R PS EQ Y + A R +V+RTLDVGGDKPL+Y+P+ E NPFLG RGIRL Sbjct: 469 QTRFPSEAEQVEVYRQVLNA-ALGRPVVMRTLDVGGDKPLSYLPI-IEENPFLGWRGIRL 526 Query: 625 CLERPQLLREQFRAIL-ASAGFARLHIMLPMVSLLSELHLARKILEEEALALGL-----T 678 L+ P+L Q RA+L AS G +LHI+LPMV L E+ A LE+ L + Sbjct: 527 TLDHPELFLVQLRAMLNASGGGEQLHILLPMVCCLDEIDQAIAYLEQAYLEVKQDVHPDL 586 Query: 679 ELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAV 738 + PK+GIM+EVP+ + A VDF S+G+NDLTQY LA+DR++PR++ DS+HP + Sbjct: 587 QRPKIGIMLEVPALLFQLEEVAKRVDFISVGSNDLTQYLLAVDRNNPRVSTLYDSYHPGI 646 Query: 739 LRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELD 798 LR + A + + VCG LA E + V +L+ +G +LS++ + I +R + Sbjct: 647 LRALTQARLACREYRLPISVCGELAGEPMGVLLLVAMGYTQLSMNQGSLAKINYLIRRVS 706 Query: 799 LADCQIIARQVLGLEEAAEVREALRQY 825 D + Q L L EVRE L Y Sbjct: 707 YQDLSELLAQALSLTNGFEVRELLTLY 733 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: 1136 Number of extensions: 45 Number of successful extensions: 5 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: 743 Length adjustment: 41 Effective length of query: 797 Effective length of database: 702 Effective search space: 559494 Effective search space used: 559494 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