Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF2318 PGA1_c23500 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::psRCH2:GFF3291 (960 letters) >FitnessBrowser__Phaeo:GFF2318 Length = 746 Score = 271 bits (694), Expect = 9e-77 Identities = 177/548 (32%), Positives = 277/548 (50%), Gaps = 15/548 (2%) Query: 408 VNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQVA 467 + G A G G V + +P+V+ + P EL+RL A++++ + +++ +Q Sbjct: 183 MRGTIAQEGAVEGHVWLHEPRVVVTNPIADDPHRELERLHEAVEELRVGVDKMLEVTQTG 242 Query: 468 SIRD--IFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLAER 525 + ++ ++ + +GLSAEAA +E A + + D L ER Sbjct: 243 DKEQLQVLEAYRMFANSKGWMRRMEEDIGRGLSAEAAVEKEQSQARARMGQVQDAYLRER 302 Query: 526 AADLRDVGRRVLACLTGVEAE---QAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGG 582 +DL D+ R+L LTG +E + P++P +L+ + P ++ + + GI+ G Sbjct: 303 LSDLDDLSNRLLRILTGQGSETGAELPEDP-VLIARNIGPGELLEYG-RNLRGIVLEEGS 360 Query: 583 ATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAA 642 SH+AIIARAL IP +V +++DGE+G + + P + R + A Sbjct: 361 VGSHAAIIARALAIPLVVHTKRITTEALNGDHIMVDGEQGVVHLRPDDTVVSAFRDKIAM 420 Query: 643 REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHS 702 + + + R A+TRDG V + N G + P GAEG+GL RTEL F+ + Sbjct: 421 QAKAQERYASIRDKQALTRDGRRVHLLMNAGLMADLPSLENSGAEGVGLFRTELQFLVRN 480 Query: 703 QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQ 762 Q P ++ A Y+RVL+A G+ +V RTLD+G DK LPY E NP LG R IR+ L Sbjct: 481 QMPKRSELVALYQRVLDAAGGKRVVFRTLDIGSDKVLPYMKPTDEPNPALGWRAIRVGLD 540 Query: 763 RPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVD-------RLRVELPVADL 815 +P ++ QL+AL+ +A+GRPL +MFP V +E+R AKA V+ RL LP L Sbjct: 541 KPGVMRMQLQALIRAANGRPLTVMFPFVAQFEEFRDAKAEVEKTLERERRLGHALP-EKL 599 Query: 816 QVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRL 875 +VG M+E PS A EV+F SIG NDL Q+ A DR + + + D L+ + L Sbjct: 600 EVGAMLETPSLAFAPQKFFDEVEFLSIGGNDLKQFFFAADRENERVRKRYDTLNVSYLSF 659 Query: 876 IGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAA 935 I VE G + CGE A + L +G+ LS+ S+ VK+ + +D Sbjct: 660 IAQIVERCEKSGTPLSFCGEDAGRPIEAVCLAAMGLRVLSMRPASVGPVKSLLMRVDLND 719 Query: 936 CQRLAQQA 943 +++ A Sbjct: 720 IRKIIADA 727 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: 1366 Number of extensions: 63 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: 746 Length adjustment: 42 Effective length of query: 918 Effective length of database: 704 Effective search space: 646272 Effective search space used: 646272 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