Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_050655247.1 C1M55_RS19650 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF4500 (838 letters) >NCBI__GCF_002893965.1:WP_050655247.1 Length = 557 Score = 298 bits (762), Expect = 7e-85 Identities = 216/568 (38%), Positives = 295/568 (51%), Gaps = 28/568 (4%) Query: 264 TQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVL 323 T S + G+ S GS ++ + PE G+ E L+ EAL + Sbjct: 2 TASVDNRIAGIGVSAGSVCAPWLRFSTPEPTSAADPITGSPEAE-----LIRIREALDAV 56 Query: 324 QDKAAGSAQ------AEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLF 377 ++ A+ AEI + D +++ A L G A A A A Sbjct: 57 AEELLSRAKTVEGVSAEILTTSAAMARDAGIVKAAKANLESGLPTAHAVAVAFDAFCEKL 116 Query: 378 QGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERA-ILIAEQLTPSQTASLDTRK 436 LG + AERA DL D+GQR + ++ G P IL+A L P+ TA+L T Sbjct: 117 TALGGYM-AERATDLRDLGQRAVAVLRGEPMPGIPAPGYPYILVARDLAPADTATLGTSD 175 Query: 437 VLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAE 496 V+G +T GG TSH AILA++LG+PA+ L LA GK ++LD G + ++P+ AE Sbjct: 176 VVGLLTAEGGPTSHTAILAKSLGIPAVVNCSGTDL-LAEGKLLILDGTTGTVTIDPS-AE 233 Query: 497 IEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLL 556 + + V A A P TRDG V ++AN+ +L++ A EGVGL Sbjct: 234 MRERAVLEASFVAEQS---ASAQGPGRTRDGFAVRLSANIGTLEDAARAGAADCEGVGLF 290 Query: 557 RSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPF 616 R+EF YL R+ APS EEQA TY ++ ++ +VVRTLD G DKPL ++ + E NP Sbjct: 291 RTEFSYLGRHDAPSVEEQAQTYASVLGHFAGQK-VVVRTLDSGSDKPLPFLDLGVEENPA 349 Query: 617 LGLRGIRLCLERPQLLREQFRAILAS--AGFARLHIMLPMVSLLSELHLARKILEEEALA 674 LG+RG+R+ P L Q A+ A+ A A L +M PMV+ E K E A + Sbjct: 350 LGIRGLRVGTVYPDTLISQLDALAAAGNATGADLWVMAPMVATADEA----KDFAELARS 405 Query: 675 LGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSF 734 G+ K+G MIEVP+AAL A H+DF SIGTNDL+QYT A+DR LA D + Sbjct: 406 RGIG---KVGAMIEVPAAALRAKDILEHLDFVSIGTNDLSQYTCAVDRMAGGLAQLLDPW 462 Query: 735 HPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATV 794 PAVL LIA +A GK VGVCG AS+ L PVL+GLGV LS+SVP + ++A + Sbjct: 463 QPAVLDLIAMVGQAGADAGKPVGVCGESASDPLLAPVLVGLGVTSLSMSVPALGAVRAQL 522 Query: 795 RELDLADCQIIARQVLGLEEAAEVREAL 822 LDLA C+ +A G E R A+ Sbjct: 523 ASLDLAVCKDMAAAARGARNPIEGRAAV 550 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: 993 Number of extensions: 42 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: 557 Length adjustment: 39 Effective length of query: 799 Effective length of database: 518 Effective search space: 413882 Effective search space used: 413882 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