Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate BPHYT_RS02575 BPHYT_RS02575 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__BFirm:BPHYT_RS02575 Length = 582 Score = 264 bits (675), Expect = 1e-74 Identities = 184/576 (31%), Positives = 285/576 (49%), Gaps = 28/576 (4%) Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLER---ALMHATQALQRLRDNA 333 L G+ S G A G +A L++ + + +ER A H L+ LR + Sbjct: 5 LHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIESEIERFRTAQQHVHYELETLRADL 64 Query: 334 AGEAQADI---FKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGST 389 A +A +++ H +L D L+++ LI + + +A E + F + Sbjct: 65 AADAPSEMGAFINVHSMILNDAMLVQETFDLIRTRRYNVEWALTEQLERLSRHFDDIEDE 124 Query: 390 LLAERALDLMDVGQRVLKLILG----VPDGVWELPDQAILIAEQLTPSQTAALDTGKVLG 445 L ER D+ V +RVLK + G + DGV D+ I++A + P+ T G Sbjct: 125 YLRERKADIEQVVERVLKALAGASVALADGVHGACDEMIVVAHDIAPADMMQFKTQTFQG 184 Query: 446 FATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQ 505 F T GG TSH AI+AR+LG+PA G+ + +++D D G + +DPA V+E+ Sbjct: 185 FVTDLGGRTSHTAIVARSLGIPAAVGVQHASALIRQDDLIIVDGDHGIVIVDPAPIVLEE 244 Query: 506 LHAKRQQQRQRHQHELENAARAAV-TRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRS 564 ++ RQ ++ Q +L+ + T G E+ AN+ + A+ GA G+GL R+ Sbjct: 245 -YSYRQSEKALEQRKLQRLKFSPTQTLCGTRIELCANIELPDDARAAIDAGATGVGLFRT 303 Query: 565 EFLYQQ-RSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVP----MDSEA 619 EFL+ + P +EQ G Y + + +RT+DVG DKPL + ++ A Sbjct: 304 EFLFMNHKDRLPEEEEQFGAYRRAVELMNGLP-VTIRTIDVGADKPLDSMSGGDGYETAA 362 Query: 620 NPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSEL-------RLARL 672 NP LG+R IR L PQ+ Q RAIL ++ + I++PM++ E+ R A+ Sbjct: 363 NPALGLRAIRWSLSEPQMFLTQLRAILRASAFGSVKILIPMLAHAQEIDQTLDLIREAKR 422 Query: 673 MLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPR 732 L++ +A ++G MIE+PAAA+ LF +DF SIGTNDL QYTLA+DR Sbjct: 423 QLDDAGMAYDPNV--QVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRADNS 480 Query: 733 LASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPL 792 +A D HP+VL LIA T++ A G V VCG +A + LLLG+G+ E S+ Sbjct: 481 VAHLYDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPTMTRLLLGMGLTEFSMHPSQ 540 Query: 793 IPAIKAAIREVELSDCQAIAHQVLGLESAEQVREAL 828 + +K + L + VL E+V+ AL Sbjct: 541 LLVVKQEVLRSHLKTLEKPVADVLASFEPEEVQAAL 576 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: 1006 Number of extensions: 56 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: 844 Length of database: 582 Length adjustment: 39 Effective length of query: 805 Effective length of database: 543 Effective search space: 437115 Effective search space used: 437115 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 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