Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate PfGW456L13_5075 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5075 Length = 953 Score = 1715 bits (4442), Expect = 0.0 Identities = 886/953 (92%), Positives = 917/953 (96%) Query: 1 MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI 60 MLELT+EQISMGQSAVDK+ ALQLLA LV DGLVA+GYLAGLQAREAQGSTFLGQGIAI Sbjct: 1 MLELTVEQISMGQSAVDKSAALQLLAGHLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI 60 Query: 61 PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 PHGTP+TRDLVF+TGVRLMQFPDGVDWGDG IVYLAIGIAAKSDEHLRLLQLLTRALGET Sbjct: 61 PHGTPETRDLVFTTGVRLMQFPDGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 Query: 121 DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180 DLGQALRRA +AEALLKLLQGAPQELALDAQMIGLGV+A+DFEELVWRGARLLRQADCVS Sbjct: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVAAEDFEELVWRGARLLRQADCVS 180 Query: 181 NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE 240 NGF+ VLQQV+ALPLGDGLWWLHSEQTVKRPGLAFVTPD+P+RYLGQPL+GLFCLASLGE Sbjct: 181 NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDRPLRYLGQPLTGLFCLASLGE 240 Query: 241 AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA 300 AHQALLERLCALLIEGRGHELGRATSSR VLEVLGGEVPADWPSARIALAN HGLHARPA Sbjct: 241 AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGEVPADWPSARIALANAHGLHARPA 300 Query: 301 KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA 360 KILAQLAKSFEG+IRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLE IAEP IAADALPA Sbjct: 301 KILAQLAKSFEGDIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEIIAEPGIAADALPA 360 Query: 361 LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV 420 LLAAIEEGLGEEVEPLP VSQ REV+AD+AEV+LAP+SGS++QAIAAAPG AIGPAHIQV Sbjct: 361 LLAAIEEGLGEEVEPLPPVSQAREVVADMAEVVLAPSSGSVVQAIAAAPGFAIGPAHIQV 420 Query: 421 QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT 480 Q IDYPLRGESA IERERL+ ALA VRRDI+GLIERSK+KAIREIFITHQEMLDDPELT Sbjct: 421 LQTIDYPLRGESAGIERERLQHALAQVRRDIQGLIERSKSKAIREIFITHQEMLDDPELT 480 Query: 481 DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP 540 DEVDTRLKQGESAEAAWMAVIEAAA+QQE+LQDALLAERAADLRDIGRRVL QLSG+ETP Sbjct: 481 DEVDTRLKQGESAEAAWMAVIEAAARQQETLQDALLAERAADLRDIGRRVLMQLSGIETP 540 Query: 541 AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV 600 +EP+QPYILVMDEVGPSDVARLDP RVAGILTARGGATAHSAIVARALGIPALVGAG V Sbjct: 541 SEPDQPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPGV 600 Query: 601 LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV 660 LLL PGT LL+DGQRGRLHVDADAATLQRAT ERDTRE RLKAAAE RHQPALT DGHAV Sbjct: 601 LLLAPGTALLLDGQRGRLHVDADAATLQRATAERDTREQRLKAAAELRHQPALTIDGHAV 660 Query: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL 720 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAH Q PDEATQEVEYRRVLDGLAGRPL Sbjct: 661 EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHPQVPDEATQEVEYRRVLDGLAGRPL 720 Query: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM 780 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQ+MEAQLRALLRAADNRPLRIM Sbjct: 721 VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM 780 Query: 781 FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840 FPMVGSVDEWRQARDMTERLR EIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND Sbjct: 781 FPMVGSVDEWRQARDMTERLRQEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND 840 Query: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL Sbjct: 841 LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL 900 Query: 901 VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL 953 VGLGVDELSV RSIAEVKARIREL TQTQTLA+QALAVGSANEVRALVEAL Sbjct: 901 VGLGVDELSVGARSIAEVKARIRELGFTQTQTLARQALAVGSANEVRALVEAL 953 Lambda K H 0.318 0.135 0.381 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: 2405 Number of extensions: 83 Number of successful extensions: 1 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: 953 Length of database: 953 Length adjustment: 44 Effective length of query: 909 Effective length of database: 909 Effective search space: 826281 Effective search space used: 826281 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: 57 (26.6 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