Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 8502167 DvMF_2877 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__Miya:8502167 Length = 591 Score = 316 bits (809), Expect = 3e-90 Identities = 195/567 (34%), Positives = 300/567 (52%), Gaps = 17/567 (2%) Query: 272 VSTKLLRGVCASAGSAFGYVVQVAERTLEM-----PEFAADQQLERESLERALMHATQAL 326 ++ ++L+G+ SAG + G R + P AAD ++ R LE+A L Sbjct: 1 MAREILQGIAVSAGVSIGKAFFTNRRRRSVSFEIIPPGAADSEVAR--LEQAASDVRDDL 58 Query: 327 QRLRDNAAGEAQ--ADIFKAHQELLEDPSLLEQAQALIAEGKSAA-FAWNSATEATATLF 383 R RDN E + A I +H + +DP L+ A I + A +A + A EA A F Sbjct: 59 ARARDNVPAELRDHAAIINSHMMICQDPKLIRAASQRIRDHHICAEWALDQAVEAIAAAF 118 Query: 384 KSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELPDQAI-LIAEQLTPSQTAALDTGK 442 ++ + ER D+ V +R+ ++G PD+ I L+A LTP+ L T K Sbjct: 119 SAIEDPYIRERVQDVRAVAERIQTRLVGRHAEPLRTPDERIVLMAHDLTPADAMGLPTVK 178 Query: 443 VLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSV 502 ++ FAT GG TSH ILAR+L +PAV G+ S+A G V++DA +G + +DP + Sbjct: 179 IMSFATAEGGKTSHTGILARSLQIPAVVGVSSLEESVADGDLVIVDALRGLIVVDPDETE 238 Query: 503 IEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLL 562 + + Q + + A T DG+ +V AN+ + E Q + G +G+GL Sbjct: 239 LADYTDLKYQFENYQKSIRRQSTLPAETLDGYRIDVQANIELVEEVPQVLDGGGDGVGLY 298 Query: 563 RSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPF 622 R+E+ + R +P+ +E YS +A L P+R +V RTLDVG DK L+ E NP Sbjct: 299 RTEYAFLNRRTSPTEEELYDEYSQLAGLLSPRR-VVFRTLDVGADKMLSEQSQLEEPNPA 357 Query: 623 LGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALALG 682 LG+R IR CL + R Q RAIL ++ ++ PM+S L ELR A+ +L E L Sbjct: 358 LGLRAIRFCLRHQDVFRRQLRAILRASAHGSASLLFPMISGLHELRQAKHILNEVRAELD 417 Query: 683 LRELP-----KLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQA 737 LP +GIM+E+P+A ++++ A EVDFFSIGTNDL QY+L +DR + ++ Sbjct: 418 AAGLPYDPDMPVGIMVELPSAVMISEALAQEVDFFSIGTNDLIQYSLGIDRGNKHVSYLY 477 Query: 738 DSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIK 797 HP+++R I V +AH G V VCG +AS+ +P+LLG+ +D +S++ IP IK Sbjct: 478 QPLHPAIVRSIKYVVDSAHRMGISVCVCGEVASDPYCLPILLGMQIDAISIAPQAIPGIK 537 Query: 798 AAIREVELSDCQAIAHQVLGLESAEQV 824 +R + +C+ + VL + + Sbjct: 538 HILRRTNMEECKELLRDVLSASTVSTI 564 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: 974 Number of extensions: 47 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: 844 Length of database: 591 Length adjustment: 39 Effective length of query: 805 Effective length of database: 552 Effective search space: 444360 Effective search space used: 444360 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