Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_086509481.1 BZY95_RS08245 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::WCS417:GFF780 (952 letters) >NCBI__GCF_002151265.1:WP_086509481.1 Length = 753 Score = 347 bits (890), Expect = 2e-99 Identities = 228/583 (39%), Positives = 332/583 (56%), Gaps = 38/583 (6%) Query: 392 LSAP-LAGSQVQ--AIAAAPGIAIGPAHIQVLQVFDYPLRGESCAIERE----RLHSALA 444 LS P L G Q + A+PG+AIG + V + D + + E RL A+ Sbjct: 163 LSKPTLPGGQAMFTGVPASPGMAIGEV-VVVAPLADLDSVPDLIPTDVEHEIARLKEAIE 221 Query: 445 DVRRDIQGLIERSQSKAIRE---IFVTHQEMLDDPELTDEVDTRLKQGESAEAAWMSVIE 501 VR +I+ ER ++ + +F +Q+ML + L+ EV+ R+++G+ A A V+ Sbjct: 222 RVREEIRAAGERLANRISAQELALFEVYQQMLSEAALSQEVEKRIREGQWAPGALADVVR 281 Query: 502 AAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQEPS---EPYILVMDEVGPSDV 558 + E + D L ERAAD+RD+GRRVLA L ET Q P+ E ILV DE+ + + Sbjct: 282 RHVQYLERVDDDYLRERAADVRDLGRRVLAHL-QEETPQTPANFPESTILVGDEISVAML 340 Query: 559 ARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVLLLAAGTPLLLDGQRGRLH 618 + R+AG+++ RG +T+H AIVARA+GIP + G L +G ++LDG RGRL Sbjct: 341 GEVPRERLAGLVSVRGSSTSHVAIVARAMGIPTVSGMVDLPLPRLSGAEVVLDGHRGRLF 400 Query: 619 VDADAATLQRATVERDTREQRLQAASAQ-----RHE---PALTRDGHAVEVFANIGESAG 670 V R + E R L A A HE P+ T DGH + + N G + Sbjct: 401 V--------RPSDELKARYSSLIAEEAALTEVLEHEQDLPSETPDGHVMPLMVNTGLAID 452 Query: 671 VASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLVVRTLDVGGDK 730 A+++++ G+GL RTE+ FM + P E Q YR L+ A P+V+RTLD+GGDK Sbjct: 453 TAASLKKRISGVGLYRTEVPFMIAERFPGEQEQARLYRDQLESFAPLPVVMRTLDIGGDK 512 Query: 731 PLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRP-LRIMFPMVGSVDEW 789 LPY+PI EE NPFLG RGIR+TL P+++ QLRA+LR+A L+I+ PMV +VDE Sbjct: 513 DLPYFPI-EEANPFLGWRGIRVTLDHPEVLMVQLRAMLRAAQGLDNLQILLPMVTNVDEV 571 Query: 790 RAARDMTERLRLEIPVADL-----QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYT 844 A + +R E+ + ++G+M+EVP+ LA+ VDFFSVG+NDLTQY Sbjct: 572 DDALRLLDRAIRELGEEGVVSPRPRVGVMLEVPATLYQLDALAERVDFFSVGSNDLTQYL 631 Query: 845 LAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGV 904 LA+DR +P +++ D HPAVL + + K + VCGELA DP +L+G+G Sbjct: 632 LAVDRNNPRVASLYDSCHPAVLCAMARLAEESRRLKKPISVCGELAGDPAGALLLMGMGF 691 Query: 905 DELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRA 947 D LS++A S+P V+A +R S+ A+ L Q+ LA+ +P VR+ Sbjct: 692 DSLSMNAPSLPRVRAAIRRVSIDAAKALVQETLALNTPVAVRS 734 Lambda K H 0.318 0.135 0.385 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: 1470 Number of extensions: 83 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 952 Length of database: 753 Length adjustment: 42 Effective length of query: 910 Effective length of database: 711 Effective search space: 647010 Effective search space used: 647010 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 24 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