Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 16910 b2829 fused PTS enzyme: PEP-protein phosphotransferase (enzyme I)/GAF domain containing protein (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_07335 (954 letters) >FitnessBrowser__Keio:16910 Length = 748 Score = 351 bits (900), Expect = e-100 Identities = 222/566 (39%), Positives = 325/566 (57%), Gaps = 18/566 (3%) Query: 403 IQAVAAAPGIAIGP----AHIQVLQAIDYPLRGESAAIERERLQNALNQVRSDIQGLIER 458 I+A+ AAPG+AI A + +++ + Y A+ERERL AL + ++ + +R Sbjct: 171 IRALPAAPGVAIAEGWQDATLPLMEQV-YQASTLDPALERERLTGALEEAANEFRRYSKR 229 Query: 459 AKAKAIRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDA 515 A A +E IF + +L D L E+ + G A+ A VIE A++ AL D Sbjct: 230 FAAGAQKETAAIFDLYSHLLSDTRLRRELFAEVDKGSVAEWAVKTVIEKFAEQFAALSDN 289 Query: 516 LLAERAADLRDVGRRVLAQLCGV-ETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTA 574 L ERA DLR +G+R+L L + PN + +ILV DE+ + +A L R+ G++ Sbjct: 290 YLKERAGDLRALGQRLLFHLDDANQGPNAWPERFILVADELSATTLAELPQDRLVGVVVR 349 Query: 575 RGGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEE 634 G A +H+AI+ RALGIP ++GA +L T L++DG RG L VDP+ LQ + Sbjct: 350 DGAANSHAAIMVRALGIPTVMGADIQPSVLHRRT-LIVDGYRGELLVDPEPVLLQEYQRL 408 Query: 635 RDTREQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFM 694 + ++A + + PA + G ++V N G S + +GIGL RTE+ FM Sbjct: 409 ISEEIELSRLAEDDVNLPAQLKSGERIKVMLNAGLSPEHEEKLGSRIDGIGLYRTEIPFM 468 Query: 695 AHSQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRL 754 S P E Q A+Y+ +L +P+ +RTLDVG DK LPY PI+ EENP LG RGIR+ Sbjct: 469 LQSGFPSEEEQVAQYQGMLQMFNDKPVTLRTLDVGADKQLPYMPIS-EENPCLGWRGIRI 527 Query: 755 TLQRPQVMEAQLRALLRS-ADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIP------V 807 TL +P++ Q+RA+LR+ A + L I+ PMV S+DE +AR + ER E+ + Sbjct: 528 TLDQPEIFLIQVRAMLRANAATGNLNILLPMVTSLDEVDEARRLIERAGREVEEMIGYEI 587 Query: 808 ADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAV 867 ++GIM+EVPS + P LAK VDF SVGTNDLTQY LA+DR + ++ D LHPA+ Sbjct: 588 PKPRIGIMLEVPSMVFMLPHLAKRVDFISVGTNDLTQYILAVDRNNTRVANIYDSLHPAM 647 Query: 868 LQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELS 927 L+ + + R A HG + +CGE+A DP+ V +L+GLG LS++ RS+A K +R + Sbjct: 648 LRALAMIAREAEIHGIDLRLCGEMAGDPMCVAILIGLGYRHLSMNGRSVARAKYLLRRID 707 Query: 928 LAQVQTLAQAALAVGSADDVRALVEA 953 A+ + LAQ +L A +VR V A Sbjct: 708 YAEAENLAQRSLEAQLATEVRHQVAA 733 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: 1209 Number of extensions: 55 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: 954 Length of database: 748 Length adjustment: 42 Effective length of query: 912 Effective length of database: 706 Effective search space: 643872 Effective search space used: 643872 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