Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 1937187 b3947 fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component (NCBI)
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__Keio:1937187 Length = 833 Score = 333 bits (854), Expect = 3e-95 Identities = 223/691 (32%), Positives = 354/691 (51%), Gaps = 49/691 (7%) Query: 293 HGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLS------------KLLAMGAH 340 +G+HARPA + + F +I T+ G + +L+ +LL GA Sbjct: 13 NGVHARPASHVETLCNTFSSQIEWHNLRTDRKGNAKSALALIGTDTLAGDNCQLLISGAD 72 Query: 341 RGQLLEFMAEPAIASDALPALVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQA 400 + + +++ D P + E +E+EPLP P + Sbjct: 73 EQEAHQRLSQ--WLRDEFPHCDAPLAEVKSDELEPLPVSLTNLNPQI------------- 117 Query: 401 ALRAGDQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTL 460 +RA +G S G + P+ + + E L+ L V +I Sbjct: 118 -IRARTVCSG---SAGGILTPISSLDLNALGNLPAAKGVDAEQSALENGLTLVLKNIEFR 173 Query: 461 IDESQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDK 520 + +S A+ I H+++ D +LRE + + GLS A + ++ Sbjct: 174 LLDSDGATSA-ILEAHRSLAGDTSLREHLLAGVSAGLSCAEAIVASANHFCEEFSRSSSS 232 Query: 521 LLAERAADLRDVGRRVLACLTGVEAEQAPD---EPYILVMDEVAPSDVATLNAQRVAGIL 577 L ERA D+RDV ++L + G + AP +P I + DE+ PS L+ + G+L Sbjct: 233 YLQERALDVRDVCFQLLQQIYGEQRFPAPGKLTQPAICMADELTPSQFLELDKNHLKGLL 292 Query: 578 TAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQL---- 633 GG TSH+ I+AR+ IP +VG L + + +DG G ++V P A Sbjct: 293 LKSGGTTSHTVILARSFNIPTLVGVDIDALTPWQQQTIYIDGNAGAIVVEPGEAVARYYQ 352 Query: 634 EQARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLR 693 ++AR + A RE+++ ++ A T DG +EIAANI + E A GAEG+GL R Sbjct: 353 QEARVQDALREQQRVWLTQQ----ARTADGIRIEIAANIAHSVEAQAAFGNGAEGVGLFR 408 Query: 694 TELVFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLG 753 TE+++M+ + AP ++ + + LE+ GR ++VRT+D+GGDKP+ Y +PAE NPFLG Sbjct: 409 TEMLYMDRTSAPGESELYNIFCQALESANGRSIIVRTMDIGGDKPVDYLNIPAEANPFLG 468 Query: 754 VRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDE--W---RTAKAMVDRLRV 808 R +R+ + + TQLR++L ++ L+IM PM+ +++E W + A+A Sbjct: 469 YRAVRIYEEYASLFTTQLRSILRASAHGSLKIMIPMISSMEEILWVKEKLAEAKQQLRNE 528 Query: 809 ELPVAD-LQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADG 867 +P + +Q+GIM+E+PS I +E+DFFSIG+NDLTQY LA+DR + ++ + Sbjct: 529 HIPFDEKIQLGIMLEVPSVMFIIDQCCEEIDFFSIGSNDLTQYLLAVDRDNAKVTRHYNS 588 Query: 868 LHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKAR 927 L+PA LR + V+A H GKW+G+CGEL A +PLLVGLG+DELS+SA SI KAR Sbjct: 589 LNPAFLRALDYAVQAVHRQGKWIGLCGELGAKGSVLPLLVGLGLDELSMSAPSIPAAKAR 648 Query: 928 VRELDFAACQRLAQQALMLPGAHEVRAFVGE 958 + +LD C++L QA+ + EV + + Sbjct: 649 MAQLDSRECRKLLNQAMACRTSLEVEHLLAQ 679 Score = 50.1 bits (118), Expect = 6e-10 Identities = 36/101 (35%), Positives = 49/101 (48%), Gaps = 6/101 (5%) Query: 43 LRAREAQGSTFLGQGIAIPHGTPETRDQVFTTGVRLLHFPAGVDWGNGQ---LVYLAIGI 99 L AREA ST LG AIPH E +Q + RL A V WG+ + ++ L + Sbjct: 731 LWAREAVFSTGLGFSFAIPHSKSEHIEQSTISVARL---QAPVRWGDDEAQFIIMLTLNK 787 Query: 100 AARSDEHLRLLQLLTRALGEGDLSEGLQQAESPEAIIGLLQ 140 A D+H+R+ L R + + L A S +AI LLQ Sbjct: 788 HAAGDQHMRIFSRLARRIMHEEFRNALVNAASADAIASLLQ 828 Lambda K H 0.317 0.134 0.384 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: 1463 Number of extensions: 63 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: 960 Length of database: 833 Length adjustment: 43 Effective length of query: 917 Effective length of database: 790 Effective search space: 724430 Effective search space used: 724430 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