Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate SMc02437 SMc02437 phosphoenolpyruvate phosphotransferase PTSP (enzyme I-Ntr) protein
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__Smeli:SMc02437 Length = 755 Score = 282 bits (722), Expect = 5e-80 Identities = 191/553 (34%), Positives = 294/553 (53%), Gaps = 20/553 (3%) Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLI---DES 464 + G + GI +G V++ +P+++ E ELQRL AL + I ++ D S Sbjct: 183 IEGNSYGEGIGLGYVVLHEPRIVVTNLLNEDTEHELQRLAEALGSLRISIDDMLSRRDVS 242 Query: 465 QVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEA-LHDKLLA 523 R + T++ D +++ ++ GL+AEAA +E ++S + + L D L Sbjct: 243 MEGEHRAVLETYRMFAHDRGWVRKLEEAIRNGLTAEAA-VERVQSETKARMIRLTDPYLR 301 Query: 524 ERAADLRDVGRRVLACLTGVEAE-QAPDEPY--ILVMDEVAPSDVATLNAQRVAGILTAG 580 ER D D+ R+L L+G A+ A D P I+V + +++ + V G++ Sbjct: 302 ERMHDFDDLANRLLRQLSGYGAKLSAADFPNDAIVVARAMGAAELLDYPRENVRGLVLEE 361 Query: 581 GGATSHSAIIARALGIPAIVGAGPGVLGLARNT-LLLLDGERGELLVAPSGAQLEQARSE 639 G TSH I+ARA+GIP +VG G + LA N +++DG+ ++ + P A L++A E Sbjct: 362 GAVTSHVVIVARAMGIP-VVGQAAGAVALAENRDAIIVDGDDAKVHLRPM-ADLQRAYEE 419 Query: 640 RAAREERKHLANERRMDAA-VTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVF 698 + R+ D +T+DG + + N G + P GAEGIGL RTEL F Sbjct: 420 KVRFRARRQAQFRALRDVEPLTKDGKRITLQMNAGLLVDLPHLNEAGAEGIGLFRTELQF 479 Query: 699 MNHSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIR 758 M S P QEA YR V++ G+P+ RTLD+GGDK +PY+ EENP LG R IR Sbjct: 480 MIASTMPKAEEQEAFYRNVMKQTAGKPVTFRTLDIGGDKVVPYFRAAEEENPALGWRAIR 539 Query: 759 LSLQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMV-------DRLRVELP 811 LSL RP +L TQ RA+L + G L++M PMV + E ++A+ ++ +L +LP Sbjct: 540 LSLDRPGLLRTQFRAMLRATAGAELKMMLPMVTEVAELKSARELLQKEIERQSKLGEQLP 599 Query: 812 VADLQVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPA 871 LQ G M+E+P+ L EVDF S+G+NDL Q+ +A+DRG+ +S + D L Sbjct: 600 -RKLQFGAMLEVPALLWQLDELMAEVDFVSVGSNDLFQFAMAVDRGNARVSERFDILGRP 658 Query: 872 VLRLIGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVREL 931 LR++ V A + V +CGE+A+ L+ L+GLG +S+S ++ VKA + L Sbjct: 659 FLRILREIVRAGERNNTPVTLCGEMASKPLSAMALLGLGFRSVSMSPTAVGPVKAMLLAL 718 Query: 932 DFAACQRLAQQAL 944 D L + AL Sbjct: 719 DAGRLNELLEAAL 731 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: 1340 Number of extensions: 73 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: 755 Length adjustment: 42 Effective length of query: 918 Effective length of database: 713 Effective search space: 654534 Effective search space used: 654534 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