Align Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized)
to candidate BPHYT_RS02740 BPHYT_RS02740 PTS glucose transporter subunit IIA
Query= SwissProt::P45597 (838 letters) >FitnessBrowser__BFirm:BPHYT_RS02740 Length = 854 Score = 474 bits (1219), Expect = e-137 Identities = 295/715 (41%), Positives = 405/715 (56%), Gaps = 28/715 (3%) Query: 135 DDPAVIVAALTGDRAPDTSAAPATDLAE--RFEWTIAYPSGLHARPATRWAETARGFSAR 192 + P +++ A G A + +T++ E R + T+ + GLHARPA R E ARGF AR Sbjct: 149 ETPLLVLRARDGAAAEASRQLSSTNVTEEARQQVTLVHAGGLHARPAARAREAARGFDAR 208 Query: 193 AQVRAGDQAADAKSLVGLLQLGLRAGDSITVSAKGSDAPALLKRLRAVMDSLTAQEKADA 252 +VR + A +S+VGLL LG AG+ TV G P + A+ + LT + + Sbjct: 209 VEVRYEGRKAAIESVVGLLGLG--AGEGATVELLGM-GPQAAAAVAAIANELTREAHGEV 265 Query: 253 ERAAQRRAAPVIGWTPPQA--QPA--------IVGIGASPGVAIGIVHRLRAAQTEVADQ 302 E R+++P PQA +PA + G+ A+PGVA+G + R A + ++ Sbjct: 266 EEKPARQSSPA-----PQAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEK 320 Query: 303 PIGLGDG-GVLLHDALTRTRQQLAAIQDDTQRRLGASDAAIFKAQAELLNDTDLITRTCQ 361 G LL A+ L D +R +A IF LL D L+ Sbjct: 321 ANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARD 380 Query: 362 LMVEGHGVAWSWHQAVEQIASGLAALGNPVLAGRAADLRDVGRRVLAQLDPAAAGAGLTD 421 L+ G ++W +A+ + L + + +LA RAADLRD+ +RVL L +A A Sbjct: 381 LISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATA--RT 438 Query: 422 LPEQPCILLAGDLSPSDTANLDTDCVLGLATAQGGPTSHTAILSRTLGLPALVAAGGQLL 481 LPE+ +L A + +PSD + LD V L A+GG TSH AIL+R G+PALVA G L Sbjct: 439 LPEE-AVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALH 497 Query: 482 DIEDGVTAIIDGSSGRLYINPSELDLDAARTHIAEQQAIREREAAQRALPAETTDGHHID 541 I +G +++ ++GRL P+ELD++ AR +RE A T+DG I+ Sbjct: 498 AIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIE 557 Query: 542 IGANVNLPEQVAMALTQGAEGVGLMRTEFLFLERGSTPTEDEQYQTYLAMARALDGRPLI 601 + AN+ + A+ GA+ VGL+RTE LF+ R + PT DE Q+Y A+ AL GR I Sbjct: 558 VAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAI 617 Query: 602 VRALDIGGDKQVAHLELPHEENPFLGVRGARLLLRRPDLLEPQLRALYRAAKDGARLSIM 661 +R LD+G DK+V +L LP E NP LG+RG RL RPDLL+ QLR L GA + I+ Sbjct: 618 IRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGA-VRIL 676 Query: 662 FPMITSVPELISLREICARIRAELDAPE-LPIGIMIEVPAAAAQADVLARHADFFSIGTN 720 PM+T V ELI +R+ EL E + +G+MIEVP+AA AD LA+HADF SIGTN Sbjct: 677 LPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTN 736 Query: 721 DLTQYVLAIDRQNPELAAEADSLHPAVLRMIRSTIDGARKHDRWVGVCGGLAGDPFGASL 780 DLTQY LA+DR +LAA+AD LHPAVLR+I +T+ GA KH +WVGVCG LAGDP L Sbjct: 737 DLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPL 796 Query: 781 LAGLGVQELSMTPNDIPAVKARLRGRALSALQQLAEQALQCETAEQVRALEAQRE 835 L GLGV ELS+ P +P +KAR+R +Q A+ AL E+A+ VRA A RE Sbjct: 797 LVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRA--ASRE 849 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: 1627 Number of extensions: 71 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: 854 Length adjustment: 42 Effective length of query: 796 Effective length of database: 812 Effective search space: 646352 Effective search space used: 646352 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