Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_007154189.1 MDG893_RS12690 phosphoenolpyruvate--protein phosphotransferase
Query= TCDB::Q9HY55 (956 letters) >NCBI__GCF_000170835.1:WP_007154189.1 Length = 942 Score = 865 bits (2236), Expect = 0.0 Identities = 486/952 (51%), Positives = 609/952 (63%), Gaps = 12/952 (1%) Query: 1 MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60 ML L IR+G A D AL L G P Y G+ ARE Q ST LG GIAI Sbjct: 1 MLTLTANDIRLGCTATDWQAALNQASQELQDAGRTTPDYHAGMLAREQQSSTVLGNGIAI 60 Query: 61 PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120 PHGTP++R+ V STG+R+LQFP GV W D VY+ + IAA+SDEHL +L+ LTR L + Sbjct: 61 PHGTPESRDAVTSTGIRVLQFPGGVTWHDNATVYVLVAIAAQSDEHLDILRHLTRVLDKP 120 Query: 121 DLGPALSAAASAEEVLGLLQGAPQELALDAQLVGLGQNAEDLDELAWLGARLLKKAGCVE 180 L L+ A E ++ LL P DAQ + LG N ELA A L+ GCV+ Sbjct: 121 GLSQKLAEADDTEALVSLLSKEPVVPKCDAQTLCLGVNTRATSELAISAAARLQGLGCVD 180 Query: 181 NGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCLASLGE 240 F + P+ LG G +H RP LA TP +P + G+FCLA G+ Sbjct: 181 ASFMKEIVSQPPVSLGQGFWLVHHSVGSIRPALALATPKEPRDD----LAGVFCLAGPGD 236 Query: 241 AHQALLERLCDLLLEGRGAELVRATSSRSVLAALGGELPPDWPSARAVLANPHGLHARPA 300 + LLER+ + L + E S +VL+ L GE + S R L N HGLHARPA Sbjct: 237 DCRELLERIDNFLAQNIPLE---NQSVDTVLSRLSGE-QANAVSDRVCLLNTHGLHARPA 292 Query: 301 QALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPA 360 + L Q A+ +IR+RL D + VSA SL++++ LGARRGQTL SA AE A+ A Sbjct: 293 KQLVQEARQHKADIRIRLEDGDGNSVSATSLTRIIGLGARRGQTLIISATGDDAEQAVAA 352 Query: 361 LLAAVREGLGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQ 420 + A+ +GLGE V L ++ A E E P PL E L+A+AASPG+A PA V Sbjct: 353 VCQAINDGLGETVSPLRQQQSQPAPAEPE----PEPLADDEPLKAVAASPGLALAPAFVM 408 Query: 421 VAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREMLDDPEL 480 ++ + RL RA D ++ L+ ++ I H EML D +L Sbjct: 409 RQPTLDYPATASDAGEQTSRLGRAIDEADGQLRTLIRQAEGGEAAPILSVHVEMLQDDDL 468 Query: 481 AEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCGVEA 540 + +N G SAEA W ++ +A QEAL D LLAERAADLRD+GRRVLA LCGV Sbjct: 469 YQAALEAINEGASAEAGWWLAIDTAARAQEALADRLLAERAADLRDVGRRVLANLCGVAM 528 Query: 541 PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALVGAGAA 600 P P++PY+LV D++GPSDVARLD QRV G++TARGGATSHSAI+ARALG+PA+VGAG Sbjct: 529 PTPPDEPYVLVADDLGPSDVARLDTQRVRGLITARGGATSHSAILARALGLPAVVGAGDR 588 Query: 601 VLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPARTRDGHA 660 +L + GT L++DGE G L P E+ + D + QA A R EPA T DGH Sbjct: 589 ILTISSGTVLVVDGERGCLVPNPGAERRDRIDRRLDQLTRLQADAHECRNEPATTTDGHT 648 Query: 661 VEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDALDGRP 720 ++VCANLG+TA AV+ GA+G+GLLRTEF+FM + APDL TQ EYR DAL+G P Sbjct: 649 IDVCANLGNTAHTPDAVDRGADGIGLLRTEFIFMEHPDAPDLDTQVKEYRHAFDALNGLP 708 Query: 721 LVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAAGERPLRV 780 LVARTLDVGGDKPL YWP+PHE+NP+LGLRGIRL+L RP+ILETQ+RAL AA RPLR+ Sbjct: 709 LVARTLDVGGDKPLDYWPLPHEDNPFLGLRGIRLSLTRPEILETQVRALLTAADNRPLRI 768 Query: 781 MFPMVGSLDEWRQARDLALRLREEIPLADLQLGIMVEVPSAALLAPVLAREVDFFSVGTN 840 MFPMV L+E+R A+ + R+R EIP LQ+G+M+EVPS ALLA LA EVDFFSVGTN Sbjct: 769 MFPMVKDLEEFRAAKAIVERVRAEIPCQGLQVGVMIEVPSCALLAHTLAPEVDFFSVGTN 828 Query: 841 DLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAADPLALPL 900 DLTQYTLAIDRGH LSA++DGLHP+VLQLI MTV AAHA +WVG+CGELA+DP A+P+ Sbjct: 829 DLTQYTLAIDRGHGQLSAESDGLHPSVLQLIRMTVEAAHAHQRWVGICGELASDPQAIPV 888 Query: 901 LVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVRALVE 952 L+GL VDELSV++R + LVKA +R L AR A+ ALG A+AAEVR +E Sbjct: 889 LLGLDVDELSVTSRRVPLVKACIRGLSRENAREQAKLALGKATAAEVRDALE 940 Lambda K H 0.318 0.134 0.382 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: 1822 Number of extensions: 64 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: 956 Length of database: 942 Length adjustment: 44 Effective length of query: 912 Effective length of database: 898 Effective search space: 818976 Effective search space used: 818976 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 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