Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate Ac3H11_2115 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2115 Length = 585 Score = 301 bits (772), Expect = 6e-86 Identities = 201/571 (35%), Positives = 289/571 (50%), Gaps = 35/571 (6%) Query: 402 IQAIAAAPGIAIGPAHIQVQQVID---YPLRGESAAIERERLKQALADVRRDIEGLIERS 458 + +A A GIAIG A + +D Y + E ER++Q V +++ L Sbjct: 5 VHGLAVARGIAIGRAVLVASSRVDVAHYFVEPSQVEGEIERVRQGRNAVVEELQRLQTDM 64 Query: 459 KAKAIREIFI---THQEMLDDPELTDEVDTRLKQG-ESAEAAWMAVIEAAAKQQESLQDA 514 A E+ H +L D LT V + + +AE A +E A+Q + ++D Sbjct: 65 PTDAPHELTALLDVHLMLLQDEALTGGVKHWITERLYNAEWALTTQLEVIARQFDEMEDE 124 Query: 515 LLAERAADLRDIGRRVLAQLSGVETPAEP-------------------EQPYILVMDEVG 555 L ER ADL + R+L + GV +P P + P +LV ++ Sbjct: 125 YLRERKADLEQVVERILRHMKGVASPVAPPASSPRRKTQQDLLLDDTVDVPLVLVAHDLS 184 Query: 556 PSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQR 615 P+D+ + + AG +T GG T+H+AIVAR++ IPA+VGA AA L++ ++IDG Sbjct: 185 PADMLQFKQSVFAGFVTDVGGKTSHTAIVARSMDIPAVVGARAASQLVRQDDWVIIDGDA 244 Query: 616 GRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSA 675 G + VD L + EL + A RH PA+T DGH +E+ ANI + +A Sbjct: 245 GVVIVDPSPIILAEYGFRQRQVELERERLARLRHTPAITIDGHKIELLANIEQPGDAAAA 304 Query: 676 VEQGAEGIGLLRTELIFMAHS-QAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLP 734 V GA G+GL R+E +FM S P E Q Y +DG+ G P+ +RT+DVG DKPL Sbjct: 305 VRAGAVGVGLFRSEFLFMGKSGNLPGEDEQYRAYCEAIDGMQGLPVTIRTIDVGADKPLD 364 Query: 735 YWPIAKEE--NPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQ 792 K+ NP LG+R IR +L P + QLRA+LRAA + + ++FPM+ E +Q Sbjct: 365 N-KAHKDNYLNPALGLRAIRWSLADPAMFRTQLRAVLRAAAHGKVNLLFPMLAHTHEIQQ 423 Query: 793 ARDMTERLRLEI-----PVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLA 847 + R E+ P +QLG MIEVP+AAL+ K DF S+GTNDL QYTLA Sbjct: 424 TLAQVDLARAELDARGEPYGPVQLGAMIEVPAAALMVRTFLKYFDFLSIGTNDLIQYTLA 483 Query: 848 IDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDE 907 IDR ++ D LHPAVL+L+ + GK V VCGE A D +L+GLG+ Sbjct: 484 IDRADEAVAHLYDPLHPAVLRLVGDVIAEGERQGKSVCVCGETAGDVTMTRLLLGLGLRS 543 Query: 908 LSVSGRSIAEVKARIRELSLTQTQTLAQQAL 938 S+ I +K + + AQQ + Sbjct: 544 FSMHPAQILAIKQEVLRADTRKLAPWAQQVI 574 Lambda K H 0.318 0.135 0.381 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: 1087 Number of extensions: 48 Number of successful extensions: 4 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: 953 Length of database: 585 Length adjustment: 40 Effective length of query: 913 Effective length of database: 545 Effective search space: 497585 Effective search space used: 497585 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