Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 16515 b2416 PEP-protein phosphotransferase of PTS system (enzyme I) (NCBI)
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__Keio:16515 Length = 575 Score = 389 bits (998), Expect = e-112 Identities = 232/567 (40%), Positives = 339/567 (59%), Gaps = 17/567 (2%) Query: 408 VNGIAASPGIAIGPVLVRKPQ--VIDYPKRGESPVI-ELQRLDAALDKVHADIGTL---I 461 ++GI ASPGIA G L+ K VID K V E++R + K A + T+ Sbjct: 2 ISGILASPGIAFGKALLLKEDEIVIDRKKISADQVDQEVERFLSGRAKASAQLETIKTKA 61 Query: 462 DESQVASIRDIFTTHQAMLKDPALREEVQVRLQ-KGLSAEAAWMEEIESAAQQQEALHDK 520 E+ IF H +L+D L +E+ ++ K ++A+AA E IE A E L D+ Sbjct: 62 GETFGEEKEAIFEGHIMLLEDEELEQEIIALIKDKHMTADAAAHEVIEGQASALEELDDE 121 Query: 521 LLAERAADLRDVGRRVLACLTGVEAEQ--APDEPYILVMDEVAPSDVATLNAQRVAGILT 578 L ERAAD+RD+G+R+L + G++ A + ILV ++ PS+ A LN ++V G +T Sbjct: 122 YLKERAADVRDIGKRLLRNILGLKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFIT 181 Query: 579 AGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARS 638 GG TSH++I+AR+L +PAIVG G + + L+LD ++ V P+ +++ R+ Sbjct: 182 DAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRA 241 Query: 639 -ERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELV 697 + E+ LA + + A +T DGH VE+ ANIG + A GAEG+GL RTE + Sbjct: 242 VQEQVASEKAELAKLKDLPA-ITLDGHQVEVCANIGTVRDVEGAERNGAEGVGLYRTEFL 300 Query: 698 FMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGI 757 FM+ P + Q A Y+ V EA + ++VRT+D+GGDK LPY P EENPFLG R I Sbjct: 301 FMDRDALPTEEEQFAAYKAVAEACGSQAVIVRTMDIGGDKELPYMNFPKEENPFLGWRAI 360 Query: 758 RLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVA---- 813 R+++ R +IL QLRA+L ++ LRIMFPM+ +++E R + ++ + EL Sbjct: 361 RIAMDRREILRDQLRAILRASAFGKLRIMFPMIISVEEVRALRKEIEIYKQELRDEGKAF 420 Query: 814 --DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPA 871 +++G+M+E P+AA IA LA+EVDFFSIGTNDLTQYTLA+DRG+ +S + P+ Sbjct: 421 DESIEIGVMVETPAAATIARHLAKEVDFFSIGTNDLTQYTLAVDRGNDMISHLYQPMSPS 480 Query: 872 VLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVREL 931 VL LI ++A+HA GKW G+CGELA D A LL+G+G+DE S+SA SI +K +R Sbjct: 481 VLNLIKQVIDASHAEGKWTGMCGELAGDERATLLLLGMGLDEFSMSAISIPRIKKIIRNT 540 Query: 932 DFAACQRLAQQALMLPGAHEVRAFVGE 958 +F + LA+QAL P E+ V + Sbjct: 541 NFEDAKVLAEQALAQPTTDELMTLVNK 567 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: 989 Number of extensions: 38 Number of successful extensions: 5 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: 960 Length of database: 575 Length adjustment: 40 Effective length of query: 920 Effective length of database: 535 Effective search space: 492200 Effective search space used: 492200 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: 55 (25.8 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