Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_051305559.1 G494_RS22685 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_000429965.1:WP_051305559.1 Length = 600 Score = 305 bits (782), Expect = 4e-87 Identities = 207/597 (34%), Positives = 316/597 (52%), Gaps = 48/597 (8%) Query: 268 ATLLRGVCASPGSAFGQVVQVT-----------DPELVITEQGTGGATERAALTRGLLAA 316 +TLL+G+ S G G+VV + PE + E A + + A Sbjct: 15 STLLQGIGVSAGIVVGRVVVIKRQTCRAGWYQLPPEFI--------QEEVARFQQAVTTA 66 Query: 317 NEALQVLQDKAAGSA--QAEIFRAHQELLEDPTLLEHAHRLLG-EGKSAAFAWNSATLAT 373 + L+ L++ A I +H +L+D + + ++ + +A +A A Sbjct: 67 EQELRQLRENLADDLADSLSIIDSHILMLKDRMIYDQTVEIIRLKNVNAEWALAQALTKV 126 Query: 374 VTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDL-PERAILIAEQLTPSQTASL 432 F + + I ER AD+ V RV ++ G + E +++A +P T L Sbjct: 127 KQRFDTIADPYIKERYADVKHVADRVFGILFGREPYQLVTGQEPVVVVANDFSPEDTMQL 186 Query: 433 DTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEP 492 T +LG + GG TSH +I+AR+L +PA+ G+ ++A G V++D D G + + P Sbjct: 187 HTENILGLLAERGGMTSHTSIVARSLNIPAVIGLTHITGSIATGDLVIIDGDAGTVIVAP 246 Query: 493 NLAEIEQLEAARKH--QVLRHQRDVAQ-ASLPATTRDGHHVEVTANVASLQEVEHALTLG 549 + EQ++A R+ ++ ++AQ L ATT DG+ V+++ANV +E+ L G Sbjct: 247 SP---EQIKAYRRQALELNAGAGELAQYIPLSATTFDGYQVQLSANVEMTEELASVLRFG 303 Query: 550 GEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGT--ERNLVVRTLDVGGDKPLAYV 607 +G+GL RSEF + ++ P ++A YT + L T + VRTLDVGGDK L ++ Sbjct: 304 SQGIGLFRSEFDFFHQSCHP---DEAALYTTYRQLLETLAPHPVTVRTLDVGGDKFLDHL 360 Query: 608 P-----MDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELH 662 P +D E NP LGLR IR L +L Q RA+L ++ RL I+ P+VS L+ELH Sbjct: 361 PGHLSQLDPERNPALGLRSIRFSLYESELFSMQLRALLRASVHGRLRILFPLVSSLAELH 420 Query: 663 LARKILEE-----EALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYT 717 + IL E L +LG+M+EVPSA ++ADVFA VDF ++GTNDL QY+ Sbjct: 421 AVKAILRTIIGQLEEDGLDYEPQVELGVMVEVPSAVILADVFAKEVDFLAVGTNDLIQYS 480 Query: 718 LAMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGV 777 LA+DR + +A+ D FHPAVLR+I T+ A HA G V VCG +A + L VL GLGV Sbjct: 481 LAIDRSNQHVAHMYDPFHPAVLRMIKQTIDAGHAQGIPVSVCGEMAGDILCATVLFGLGV 540 Query: 778 DELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREA----LRQYHAATV 830 DELS+ +IP IK +R L + Q++ +++L + +V+ LRQY+ V Sbjct: 541 DELSMRPAVIPYIKRLLRHLRYDELQLLGQEILHCVDGRQVQNQLMAFLRQYYPEKV 597 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: 996 Number of extensions: 52 Number of successful extensions: 6 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: 600 Length adjustment: 39 Effective length of query: 799 Effective length of database: 561 Effective search space: 448239 Effective search space used: 448239 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 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