Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate RR42_RS01795 RR42_RS01795 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_1146 (953 letters) >FitnessBrowser__Cup4G11:RR42_RS01795 Length = 591 Score = 313 bits (803), Expect = 2e-89 Identities = 201/587 (34%), Positives = 306/587 (52%), Gaps = 35/587 (5%) Query: 402 IQAIAAAPGIAIGPAHIQVQQVID---YPLRGESAAIERERLKQALADVRRDIEGL---I 455 + I + G+AIG AH+ +D Y + + E ERL+ A A VR ++ L + Sbjct: 5 LHGIPVSRGVAIGRAHLLAPAALDVSHYLVDEDRLDAEVERLRSARAAVRAELVTLKRDL 64 Query: 456 ERSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGE-SAEAAWMAVIEAAAKQQESLQDA 514 R + + H +LDD L E + ++ +AE A +E +Q + ++D Sbjct: 65 PREAPEELGAFLDVHAMILDDEALAREPEALIRNRRYNAEWALTTRLEELMRQFDEIEDE 124 Query: 515 LLAERAADLRDIGRRVLAQLSG--VETPA-----------EPEQPYILVMDEVGPSDVAR 561 L ER AD+R + R+L L+G V PA EP I+V ++ P+D+ + Sbjct: 125 YLRERKADIRQVVERILKVLAGAAVLAPAPVPPSSLAPDGEPAPGVIVVAHDISPADMLQ 184 Query: 562 LDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLLLKPGTPLLIDGQRGRLHVD 621 T G +T GG T+H+AIVAR+L IPA VG +A L++ ++IDG G + VD Sbjct: 185 FRHTVFHGFVTDLGGRTSHTAIVARSLDIPAAVGVQSASELIRQDDWVIIDGDAGLVIVD 244 Query: 622 ADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAVEVFANIGESAGVTSAVEQGAE 681 A L+ + R L K RH PA+T DG +++ ANI + T+A+ GA Sbjct: 245 PSAIILEEYRHRQSERALEKKRLQRLRHTPAVTLDGLEIDLLANIEMAEDATAALTAGAV 304 Query: 682 GIGLLRTELIFM-AHSQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWP--- 737 G+GL R+E +FM + PDE Q YR +D + G P+ +RT+D+G DKPL Sbjct: 305 GVGLFRSEFLFMNRRGELPDEEEQFEAYRGAVDAMHGLPVTIRTIDIGADKPLDGRDGRD 364 Query: 738 -----IAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQ 792 NP LG+R IR +L P + QLRALLRA+ P+R++ PM+ E Q Sbjct: 365 GRGDDFETALNPALGLRAIRWSLSEPAMFLTQLRALLRASAFGPVRLLIPMLAHAREIDQ 424 Query: 793 ARDMTERLRLEIPVA------DLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTL 846 D+ + + ++ ++++G MIE+P+A L+ P+ + +DF S+GTNDL QYTL Sbjct: 425 TLDLIAQAKRQLDARGQAFDPNIKVGAMIEIPAAVLMLPLFLRRMDFLSIGTNDLIQYTL 484 Query: 847 AIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVD 906 AIDR ++ D LHPAVLQLI T+R A+ G V VCGE+A DP +L+G+G+ Sbjct: 485 AIDRADNAVAHLYDPLHPAVLQLIARTIREANRAGVPVAVCGEMAGDPAMTRLLLGMGLR 544 Query: 907 ELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL 953 E S+ + VK + + + L +Q L+ E+ ++ L Sbjct: 545 EFSMHPSQLLRVKQEVLHADCERLERLVEQVLSAYEPEELACALKLL 591 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: 1154 Number of extensions: 45 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: 953 Length of database: 591 Length adjustment: 40 Effective length of query: 913 Effective length of database: 551 Effective search space: 503063 Effective search space used: 503063 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