Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components
Query= reanno::WCS417:GFF780 (952 letters) >FitnessBrowser__Putida:PP_0793 Length = 950 Score = 1439 bits (3725), Expect = 0.0 Identities = 741/950 (78%), Positives = 825/950 (86%), Gaps = 2/950 (0%) Query: 1 MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI 60 MLEL EQI+MGQ A DK+ AL LLA++LVADGLVAEGYL GLQAREAQGSTFLGQGIAI Sbjct: 1 MLELANEQIAMGQKAADKAEALRLLADRLVADGLVAEGYLQGLQAREAQGSTFLGQGIAI 60 Query: 61 PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120 PHGTP+TRD V++TGVRLLQFPEGVDWGDGQ+VYLAIGIAA+SDEHLRLLQLLTRALGET Sbjct: 61 PHGTPQTRDLVYATGVRLLQFPEGVDWGDGQMVYLAIGIAARSDEHLRLLQLLTRALGET 120 Query: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180 DL +ALRRA SAEALLKLLQGAPQ LALDAQ++GL V A+DF+EL WRGARLL++ADCV Sbjct: 121 DLAEALRRASSAEALLKLLQGAPQALALDAQLVGLNVPAEDFDELAWRGARLLQRADCVD 180 Query: 181 NGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASLGE 240 +GFAAVLQQ + LPLG+GLWWLHSE+ V++PGLAF+TP +P+RY QPLNGLFCLASLG Sbjct: 181 SGFAAVLQQAEPLPLGEGLWWLHSERQVRQPGLAFITPQQPLRYRDQPLNGLFCLASLGA 240 Query: 241 AHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPA 300 AH+ LLERLC +LIEGRGQ L +ATSSRAVLEVLGGE+P DWP+AR+ LAN HGLHARPA Sbjct: 241 AHEALLERLCEVLIEGRGQVLYQATSSRAVLEVLGGEVPADWPSARVVLANPHGLHARPA 300 Query: 301 KILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPA 360 K+LAQLAK F+G++RVR+VD AVSVKSLSKLLSLGARRGQ LE +AEPSIA DALP Sbjct: 301 KVLAQLAKGFEGEIRVRLVDSAQPAVSVKSLSKLLSLGARRGQALELVAEPSIAADALPV 360 Query: 361 LLAAVEEGLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVL 420 LLAA+E+GLGE+VEPLP SV P D+ L AP AGS++Q + AAPGIA GPAH+ V Sbjct: 361 LLAAIEQGLGEEVEPLPQ-SVAPIADDVPEVLQAPAAGSRIQGVGAAPGIASGPAHVCVE 419 Query: 421 QVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTD 480 + FDYPLRGESCA+ER++L ALA V ++Q L+ RS KAI EIFVTHQEML DP LTD Sbjct: 420 REFDYPLRGESCALERQKLREALATVNGELQALVLRSD-KAIGEIFVTHQEMLADPALTD 478 Query: 481 EVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ 540 +V+ RL QGESA AAWM+VIEAAA+QQE+L DALLAERAADLRDIGRRVLAQLCGV+ Sbjct: 479 DVEQRLAQGESAAAAWMAVIEAAARQQEALHDALLAERAADLRDIGRRVLAQLCGVQAQV 538 Query: 541 EPSEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVL 600 EP +PY+LVM EVGPSDVARLDP RVAGI+TA+GGATAHSAIVARALGIPA+VGAG ++L Sbjct: 539 EPEQPYVLVMTEVGPSDVARLDPNRVAGIVTAQGGATAHSAIVARALGIPAVVGAGASIL 598 Query: 601 LLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVE 660 LL +GTPLLLDGQRG + V A LQRA ERD REQRLQAA A R EPA+TRDGHAVE Sbjct: 599 LLESGTPLLLDGQRGVVSVAPPADELQRALAERDLREQRLQAAWANRFEPAITRDGHAVE 658 Query: 661 VFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLV 720 VFANIG+S G+A VEQGAEG+GLLRTELIFMAHPQAPD ATQEAEYRRVLDGL GRPLV Sbjct: 659 VFANIGDSNGIAKVVEQGAEGVGLLRTELIFMAHPQAPDVATQEAEYRRVLDGLDGRPLV 718 Query: 721 VRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMF 780 VRTLDVGGDKPLPYWPIA EENPFLGVRG+RLTLQRPQ+ME QLRALLR+AD RPLRIMF Sbjct: 719 VRTLDVGGDKPLPYWPIAAEENPFLGVRGVRLTLQRPQVMEDQLRALLRAADQRPLRIMF 778 Query: 781 PMVGSVDEWRAARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL 840 PMVG V EWR AR M ERLR EIPVADLQLGIM+EVPSAALLA LA+EVDFFS+GTNDL Sbjct: 779 PMVGQVHEWREARAMVERLRAEIPVADLQLGIMVEVPSAALLAAQLAREVDFFSIGTNDL 838 Query: 841 TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV 900 TQYTLAIDRGHP+LSAQADGLHPAVL LID+TVRAAHAHGKWVGVCGELAADP AV VL+ Sbjct: 839 TQYTLAIDRGHPSLSAQADGLHPAVLSLIDMTVRAAHAHGKWVGVCGELAADPQAVAVLL 898 Query: 901 GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRALVE 950 GL VDELSVSARSI EVKA VR+ A+ LA++AL S A VRALVE Sbjct: 899 GLDVDELSVSARSIAEVKALVRQADHQTARALAREALQQDSAAAVRALVE 948 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: 2363 Number of extensions: 80 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: 952 Length of database: 950 Length adjustment: 44 Effective length of query: 908 Effective length of database: 906 Effective search space: 822648 Effective search space used: 822648 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: 57 (26.6 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