Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__psRCH2:GFF3291 Length = 960 Score = 1858 bits (4813), Expect = 0.0 Identities = 960/960 (100%), Positives = 960/960 (100%) Query: 1 MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI 60 MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI Sbjct: 1 MLELNAQHIHMHQAAADKPAALALLGEVLVADGLVAAGYLEGLRAREAQGSTFLGQGIAI 60 Query: 61 PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG 120 PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG Sbjct: 61 PHGTPETRDQVFTTGVRLLHFPAGVDWGNGQLVYLAIGIAARSDEHLRLLQLLTRALGEG 120 Query: 121 DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE 180 DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE Sbjct: 121 DLSEGLQQAESPEAIIGLLQGAPQALALDGELVSLGVAADDFDELAWQGVKLLKRAQCVE 180 Query: 181 PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE 240 PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE Sbjct: 181 PGFNASLPLGQSLPLGDGLWWLSSEQSVQRPGLAFVTPVSNLEHQGQPLNGLFVLASMGE 240 Query: 241 AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA 300 AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA Sbjct: 241 AHQAMLERLCNLLIEGRGQELSQATSSRTVLEALGGDVPADWPSAQVPLANAHGLHARPA 300 Query: 301 KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA 360 KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA Sbjct: 301 KVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFMAEPAIASDALPA 360 Query: 361 LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG 420 LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG Sbjct: 361 LVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALRAGDQVNGIAASPGIAIG 420 Query: 421 PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML 480 PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML Sbjct: 421 PVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVASIRDIFTTHQAML 480 Query: 481 KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL 540 KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL Sbjct: 481 KDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAERAADLRDVGRRVLACL 540 Query: 541 TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV 600 TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV Sbjct: 541 TGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGGATSHSAIIARALGIPAIV 600 Query: 601 GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT 660 GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT Sbjct: 601 GAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAAREERKHLANERRMDAAVT 660 Query: 661 RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA 720 RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA Sbjct: 661 RDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHSQAPNQATQEAEYRRVLEA 720 Query: 721 LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG 780 LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG Sbjct: 721 LEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQRPDILETQLRALLASADG 780 Query: 781 RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF 840 RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF Sbjct: 781 RPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVGIMIEIPSAALIAPVLAQEVDFF 840 Query: 841 SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA 900 SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA Sbjct: 841 SIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVEAAHAHGKWVGVCGELAADA 900 Query: 901 LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC 960 LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC Sbjct: 901 LAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQQALMLPGAHEVRAFVGEHC 960 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: 2681 Number of extensions: 93 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: 960 Length of database: 960 Length adjustment: 44 Effective length of query: 916 Effective length of database: 916 Effective search space: 839056 Effective search space used: 839056 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