Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate BWI76_RS10675 BWI76_RS10675 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__Koxy:BWI76_RS10675 Length = 833 Score = 322 bits (826), Expect = 5e-92 Identities = 222/674 (32%), Positives = 342/674 (50%), Gaps = 26/674 (3%) Query: 293 HGLHARPAKILAQLAKSFDGD---LRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIA 349 +G+HARPA ++ L +F L +R G + KS ++ +G E I Sbjct: 13 NGVHARPASLVETLCNTFSSSVEWLNIRTE----GRGNAKSALAIIGTNTLKGDRCELIV 68 Query: 350 EPSIAGDALPALLAAVEEGLGEDVEPLPTLSVQPEVLDIEP--ELSAPLAGSQVQAIAAA 407 A AL A + + PLPT E +D++P E + L + A+ Sbjct: 69 SGEDEEQAFAALSAFIRDEFPHCDAPLPTA----EQMDVQPVPESLSRLNPTLFHALPVC 124 Query: 408 PGIAIGP-AHIQVLQVFDYPLRGESCAIERER--LHSALADVRRDIQGLIERSQSKAIRE 464 G A G H++ L + D + AIE+E+ L L + ++I+ + + A Sbjct: 125 AGSAGGRLTHLKSLDLRDLGALPAAGAIEQEQAALDKGLTLLVKNIEFRLLDNDGTA-SA 183 Query: 465 IFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRD 524 I H+ + D L + L G S A ++ E Q + ++ L ER D+RD Sbjct: 184 ILEAHRSLATDASLRQHLLDGLLSGLSCAEAVVASGEHFCAQFSASGNSYLQERVLDVRD 243 Query: 525 IGRRVLAQLCGVETSQEP---SEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSA 581 + ++L + G P +E I + DE+ PS LD + G+L GG T+H+ Sbjct: 244 VCFQLLQHIYGEARFPAPGKLTEEAICLADELTPSQFLELDKTLLKGLLLRSGGTTSHTV 303 Query: 582 IVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQ 641 I+AR+ IP LVG LL + +DG G + V+ + A + E + Q + Sbjct: 304 ILARSFNIPTLVGVDMEALLPWVDRRVQIDGNAGLVVVNPNQAVARYYQQEAWVQAQIRR 363 Query: 642 AASAQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEA 701 A + T DG +EV ANI S +A GA+ +GL RTE+++M P AP E Sbjct: 364 QQQAWLDKEGRTEDGIRLEVAANIAHSVEATAAFNNGAQSVGLFRTEMLYMDRPSAPSEN 423 Query: 702 TQEAEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIME 761 + + L+ GR +++RT+D+GGDKP+ Y I E NPFLG R +R+ + + Sbjct: 424 ELYNIFCQALEPANGRGIIIRTMDIGGDKPVAYLNIPAENNPFLGYRAVRIYAEYQALFR 483 Query: 762 AQLRALLRSADNRPLRIMFPMVGSVDE--W--RAARDMTERLRLE-IPVAD-LQLGIMIE 815 QLRA+LR++ + L+IM PM+ S++E W D + LR E IP + + LGIM+E Sbjct: 484 TQLRAILRASAHGALKIMIPMISSMEEILWVKEQLADAKQSLRSEHIPFDEKIPLGIMLE 543 Query: 816 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 875 VPS + +E+DFFS+G+NDLTQY LA+DR + ++ + L+PA L+ +D V+A Sbjct: 544 VPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNSLNPAFLRALDYAVQA 603 Query: 876 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIPEVKARVREFSLSEAQGLAQK 935 H GKW+G+CGEL A +P+LVGLG+DELS+SA SIP KAR+ + + L + Sbjct: 604 VHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPATKARLAQLDSRACRQLLNQ 663 Query: 936 ALAVGSPAEVRALV 949 A+ + EV L+ Sbjct: 664 AMQCRTSLEVEHLL 677 Score = 53.9 bits (128), Expect = 4e-11 Identities = 37/101 (36%), Positives = 52/101 (51%), Gaps = 6/101 (5%) Query: 43 LQAREAQGSTFLGQGIAIPHGTPETRDQVFSTGVRLLQFPEGVDWGDGQ---IVYLAIGI 99 L AREA ST LG AIPH E +Q + RL Q V WGD + ++ L + Sbjct: 731 LWAREAVFSTGLGFSFAIPHSKSEHIEQSTISVARLAQ---PVAWGDDEAQFVIMLTLNK 787 Query: 100 AAKSDEHLRLLQLLTRALGETDLGQALRRAGSAEALLKLLQ 140 + D+H+R+ L R + + Q+L A S+EA+ LLQ Sbjct: 788 HSAGDQHMRIFSRLARRIMHAEFRQSLVTAQSSEAIAALLQ 828 Lambda K H 0.318 0.135 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: 1395 Number of extensions: 68 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 952 Length of database: 833 Length adjustment: 43 Effective length of query: 909 Effective length of database: 790 Effective search space: 718110 Effective search space used: 718110 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: 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