Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate Ga0059261_1646 Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)
Query= SwissProt::P45597 (838 letters) >FitnessBrowser__Korea:Ga0059261_1646 Length = 830 Score = 473 bits (1216), Expect = e-137 Identities = 286/673 (42%), Positives = 379/673 (56%), Gaps = 31/673 (4%) Query: 167 TIAYPSGLHARPATRWAETARGFSARAQVRAGDQAADAKSLVGLLQLGLRAGDSITVSAK 226 T+ P G+HARPA R E AR F A + GD+ DA+S VGLL LG R GD + V A+ Sbjct: 171 TLILPHGIHARPAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQAR 230 Query: 227 GSDAPALLKRLRAVMDSLTAQEKADAERAAQRRAAPVIGWTPPQAQPA-IVGIGASPGVA 285 GSDA A L + A++ S D A A + P QP I G+ ASPG+A Sbjct: 231 GSDAEAALAAIVALLGS-------DMGEGAPAHAPAIAVPAAPVLQPGQIGGVIASPGLA 283 Query: 286 IGIVHRLRAAQTEVADQPIGLGDGGVLLHDALTRTRQQLAAIQDDTQRRLGASDAAIFKA 345 +G RLR V + G+ L A T R ++ A D G S AA+ +A Sbjct: 284 MGPAARLRQTAIAVEREGKGVDAERTALDAARTEVRVRIGARADAA----GGSVAAVMRA 339 Query: 346 QAELLNDTDLITRTCQLMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRDVGRR 405 LL+D +L + G+ ++W AV + L A GN L R DL D+ R+ Sbjct: 340 HLALLDDPELAAGAETRIAAGNSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQ 399 Query: 406 VL-------AQLDPAAAGAGLTDLPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPT 458 VL A+ D AAGA IL+A DL PS ++ G+ +GGPT Sbjct: 400 VLGVLTGIPAEADAIAAGA----------ILVADDLLPSQLVSIAASKPAGICLVRGGPT 449 Query: 459 SHTAILSRTLGLPALVAAGGQLLDIEDGVTAIIDGSSGRLYINPSELDLDAARTHIAEQQ 518 SH AIL +GLPALVA G + IEDG ++D +G + +PS+ D DA +A+++ Sbjct: 450 SHVAILCAGMGLPALVAMGDAIEAIEDGTALLLDAEAGHVTPDPSQADADAFAARLAKRE 509 Query: 519 AIREREAAQRALPAETTDGHHIDIGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGST 578 A R+ A +T DG I++ AN+ E A QGAEG GL+R+EFLFL+R Sbjct: 510 ARRDAARAAAGNACQTADGVRIELFANLGTVEDAKAAAAQGAEGSGLVRSEFLFLDREDA 569 Query: 579 PTEDEQYQTYLAMARALDGRPLIVRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRP 638 P+EDEQ+ Y +A AL G+P+IVR LD+GGDK A++ EENP LG+RG R+ L Sbjct: 570 PSEDEQHAAYQGIADALPGKPVIVRLLDVGGDKPAAYIPFDAEENPALGLRGIRVGLAHR 629 Query: 639 DLLEPQLRALYRAAKDGARLSIMFPMITSVPELISLREICARIRAELD-APELPIGIMIE 697 DLLE Q+RA+ R G + IM PM+ SV E+ ++RE+ R+R E+ + +G+M+E Sbjct: 630 DLLETQIRAILRVQPVG-QCRIMLPMVASVSEIRAVREVVERLRGEMGIETPIEVGVMVE 688 Query: 698 VPAAAAQADVLARHADFFSIGTNDLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDG 757 PAAA AD+LA ADF SIGTNDLTQYVLA+DR NP +A+ D++HPAVLRMI T Sbjct: 689 TPAAAITADLLAAEADFLSIGTNDLTQYVLAMDRGNPAVASGVDAMHPAVLRMIAETCRR 748 Query: 758 ARKHDRWVGVCGGLAGDPFGASLLAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQ 817 A RWVGVCGGLA DP +L GLG ELS P +P KA +R L+ + AE+ Sbjct: 749 ATAKGRWVGVCGGLASDPAAVPILIGLGATELSTVPGFVPEAKAIVRSVTLADARDHAER 808 Query: 818 ALQCETAEQVRAL 830 AL C +A +VRAL Sbjct: 809 ALHCSSAAEVRAL 821 Lambda K H 0.318 0.134 0.385 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: 1793 Number of extensions: 108 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: 830 Length adjustment: 42 Effective length of query: 796 Effective length of database: 788 Effective search space: 627248 Effective search space used: 627248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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