Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 5209394 Shew_1865 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__PV4:5209394 Length = 568 Score = 308 bits (788), Expect = 8e-88 Identities = 193/559 (34%), Positives = 299/559 (53%), Gaps = 28/559 (5%) Query: 408 VNGIAASPGIAIGPVLVRKP--QVIDYPKRGESPVI-ELQRLDAALDKVHADIGTLIDES 464 + GIA S GIA G V + +DY S + E QRL+ AL TLI +S Sbjct: 3 MRGIAVSAGIAFGQAKVLRTYESKLDYHLLPPSQLAREQQRLNRALK-------TLIKQS 55 Query: 465 QVASIR--------DIFTTHQAMLKDPALREEVQVRLQKG-LSAEAAWMEEIESAAQQQE 515 Q + + + +L+D L E+ + K SA A AQ + Sbjct: 56 QACAAKLDPESDNYQLIEADLLLLEDEELLAELSDTIGKRQFSAALAVEHSFAKQAQAMQ 115 Query: 516 ALHDKLLAERAADLRDVGRRVL-ACLTGV--EAEQAPDEPYILVMDEVAPSDVATLNAQR 572 LA RA D+ +G+R++ LTG + P+ +L D + P++ ATL +R Sbjct: 116 EADSPYLARRAEDVLSLGQRLIRTLLTGHCDNLSRLPENAIVLAKD-ITPAEFATLPLER 174 Query: 573 VAGILTAGGGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQ 632 V+ ++ GG TSH+AI+AR+ GIP ++ L + +L +D GEL + P Q Sbjct: 175 VSALVLQTGGVTSHTAILARSAGIPTLMSCPWQTLEVTDGMVLAVDAINGELYLEPDETQ 234 Query: 633 LEQARSERAAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLL 692 ++ +++ +ERK + T+DG + + AN+G E +GAEG+GL Sbjct: 235 IDDLNAQKQQADERKSALLALKGTVTQTKDGRSIPLLANVGCISEINHLADVGAEGVGLF 294 Query: 693 RTELVFMNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFL 752 RTE +FMN+ + P++ Q Y L+ L+G+PL +R++D+G DK +P M +EENP L Sbjct: 295 RTEFLFMNNHELPDENRQYQLYCDALQLLDGKPLTIRSMDLGADKEVPTLAMDSEENPAL 354 Query: 753 GVRGIRLSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPV 812 G+RG+R +L P + QL+A+L +A+ P+R+MFPMV ++E A+++ + EL Sbjct: 355 GLRGVRYTLAHPKLFSAQLKAILRAANHGPIRLMFPMVNQVEELEAVLALLELCKQELVE 414 Query: 813 A-----DLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADG 867 A +L++GI++E P+A + +DF SIGTNDLTQYT+A DR +P L Q Sbjct: 415 AEKGFGELELGIVVETPAAVFNLASMLPLLDFVSIGTNDLTQYTMAADRANPLLIDQYPV 474 Query: 868 LHPAVLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKAR 927 L P ++RLI +E A A V +CGELA++ A LL+GLG++E SV+ S+ VK Sbjct: 475 LSPVIIRLIAQIIEQAKAAKVRVSMCGELASNPSATALLIGLGLEEFSVNLASLLEVKQA 534 Query: 928 VRELDFAACQRLAQQALML 946 + + C LA +AL + Sbjct: 535 LSRWSYPDCVELAHKALQI 553 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: 978 Number of extensions: 42 Number of successful extensions: 2 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: 568 Length adjustment: 40 Effective length of query: 920 Effective length of database: 528 Effective search space: 485760 Effective search space used: 485760 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