Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_057508246.1 ABB28_RS08640 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_001431535.1:WP_057508246.1 Length = 585 Score = 277 bits (708), Expect = 1e-78 Identities = 191/563 (33%), Positives = 280/563 (49%), Gaps = 16/563 (2%) Query: 270 LLRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTR---GLLAANEALQVLQDK 326 LL G AS G+A G+ L + EQ L R L AA + L+ + Sbjct: 18 LLSGHGASRGTALGRARVRLAHALEVAEQRVAPQQVDKELKRLHVALDAARNEMHDLRQR 77 Query: 327 AAGSAQ---AEIFRAHQELLEDPTLLEHAHRLLGEGK-SAAFAWNSATLATVTLFQGLGN 382 G+ E H LL+DP LL L+ G SA +A +F G+ + Sbjct: 78 LQGALNQEAGEFLDLHALLLDDPELLFGLDELIRSGPYSAGYALRLQRDRLAKVFDGMDD 137 Query: 383 ALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVT 442 A + R DL V R+ + + A IL+ + + PS+ A L ++ V+ VT Sbjct: 138 AYLKSRMDDLDHVIGRIHAFLQPVLPPAVKGLAGEILVCDNIAPSEMAQLQSQGVVAIVT 197 Query: 443 VAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEA 502 AG A SH AILAR+L LP I VP + +++G +++D G + + P + Sbjct: 198 TAGSALSHSAILARSLHLPLIVNVPGLLHKVSDGDVLIVDGSDGSITVNPQAENLRDYRV 257 Query: 503 ARKHQVLRHQRDVAQA-SLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFL 561 K R QR++ + S P+ TRD + + AN SL++V A G +G+GL R+EFL Sbjct: 258 RLKEHA-REQRELGRLRSKPSRTRDQVDIALLANAESLEDVTQAHAFGAQGLGLYRTEFL 316 Query: 562 YLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDK-PLAYVPMDAETNPFLGLR 620 +L RN P EEQ TY A + R + +RTLD+G DK + + E NP LGLR Sbjct: 317 FLQRNELPDEEEQFHTYRDAALGM-AGRLVTIRTLDLGADKADRTGLTLSNEENPALGLR 375 Query: 621 GIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSEL-----HLARKILEEEALAL 675 G+RL L RP + Q RAIL ++ + ++ I++PMVS EL + R + A Sbjct: 376 GVRLSLARPLVADTQLRAILRASAYGKVRILIPMVSTREELLAVRRRMTRLTAQLRAEGH 435 Query: 676 GLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFH 735 ++E LG MIEVP+AA + F VDF SIGTNDL QY LA DR++ L H Sbjct: 436 AVSERVPLGAMIEVPAAAFALESFIDLVDFLSIGTNDLVQYLLAADRNNEALGELYSPLH 495 Query: 736 PAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVR 795 PAVLRL+ ++ H V VCG +A +A P+L+ LG+ E S+ + ++ +R Sbjct: 496 PAVLRLLKLVIETGQRHQIPVAVCGEIAGDARLAPLLLALGLTEFSLHPGTLLEVRRAIR 555 Query: 796 ELDLADCQIIARQVLGLEEAAEV 818 E DL + + A ++L + + Sbjct: 556 ESDLGELRARAPKLLAARDRRSI 578 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: 1000 Number of extensions: 53 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: 838 Length of database: 585 Length adjustment: 39 Effective length of query: 799 Effective length of database: 546 Effective search space: 436254 Effective search space used: 436254 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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