Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate H281DRAFT_02007 H281DRAFT_02007 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__Burk376:H281DRAFT_02007 Length = 582 Score = 258 bits (658), Expect = 9e-73 Identities = 187/584 (32%), Positives = 287/584 (49%), Gaps = 32/584 (5%) Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEFA---ADQQLERESLERALMHATQALQRLRDNA 333 L G+ S G A G +A L++ + A + E E A + L LR + Sbjct: 5 LHGIPVSRGIAIGRAYLIAPAALDVDHYLIEPAQIESEVERFRAAQQRVHEELDALRADL 64 Query: 334 AGEAQADI---FKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGST 389 A +A +++ H +L D L+++ LI + + +A E + F + Sbjct: 65 AADAPSEMGAFINVHSMILNDAMLVQETIDLIRTRRYNVEWALTEQLERLSRHFDDIEDE 124 Query: 390 LLAERALDLMDVGQRVLKLILGVP----DGVWELPDQAILIAEQLTPSQTAALDTGKVLG 445 L ER D+ V +RVLK + G +GV D+ I++A + P+ T G Sbjct: 125 YLRERKADIEQVVERVLKALAGASGSLVNGVHGACDEMIVVAHDIAPADMMQFKTQTFQG 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 -YSYRQSEKALEQRKLQRLKFSPTQTLCGTRIELCANIELPEDARAAVDAGATGVGLFRT 303 Query: 565 EFLYQQ-RSVAPSHDEQAGTYSAIARALGPQRNL--VVRTLDVGGDKPLAYVP----MDS 617 EFL+ + P +EQ + A RA+ L +RT+DVG DKPL + ++ Sbjct: 304 EFLFMNHKHRMPEEEEQ---FEAYRRAVELMNGLPVTIRTIDVGADKPLDSMSGGDGYET 360 Query: 618 EANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSEL-------RLA 670 ANP LG+R IR L PQ+ Q RAIL ++ + I++PM++ E+ R A Sbjct: 361 AANPALGLRAIRWSLSEPQMFLTQLRAILRASAFGTVKILVPMLAHAQEIDQTLDLIREA 420 Query: 671 RLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDH 730 + L++ +A ++G MIE+PAAA+ LF +DF SIGTNDL QYTLA+DR Sbjct: 421 KRQLDDAGIAYDPNV--QVGAMIEIPAAAIALPLFLKRLDFLSIGTNDLIQYTLAIDRAD 478 Query: 731 PRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSV 790 +A D HP+VL LIA T++ A G V VCG +A + LLLG+G+ E S+ Sbjct: 479 NSVAHLYDPLHPAVLHLIAFTLREAKRAGVPVSVCGEMAGDPSLTRLLLGMGLTEFSMHP 538 Query: 791 PLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQA 834 + +K + L + VL E+V+ AL QA Sbjct: 539 SQLLVVKQEVLRSHLKTLEKPVADVLASFEPEEVQAALKRVAQA 582 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: 1003 Number of extensions: 51 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