Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components
Query= TCDB::Q9HY55 (956 letters) >FitnessBrowser__Marino:GFF3781 Length = 978 Score = 867 bits (2239), Expect = 0.0 Identities = 480/953 (50%), Positives = 624/953 (65%), Gaps = 11/953 (1%) Query: 1 MLELDTRQIRMGQRAADKAEALRLLGAALVADGLAAPGYAEGLKAREAQGSTYLGQGIAI 60 ML L +R+G A+D +AL+ L G +P Y G+ ARE Q ST LG GIAI Sbjct: 36 MLTLTANDVRLGATASDWQDALQQAARDLERAGRTSPEYLAGMNAREQQSSTVLGNGIAI 95 Query: 61 PHGTPDTRELVFSTGVRLLQFPEGVDWGDGQQVYLAIGIAAKSDEHLQLLQLLTRALGEA 120 PHGTP++R+ V TGVR+LQFPEGV W DG +V++ + IAA+SDEHL +L+ LTR L + Sbjct: 96 PHGTPESRDAVLETGVRILQFPEGVSWHDGARVHVLVAIAAQSDEHLDILRHLTRVLDKP 155 Query: 121 DLGPALSAAASAEEVLGLLQGAPQELALDAQLVGLGQNAEDLDELAWLGARLLKKAGCVE 180 L L A A E++ LL AP D++ + LG +A +ELA + A L+ CV+ Sbjct: 156 GLAEKLGHATDATELVALLSKAPAVAKCDSETLCLGIDASTPNELALIAAARLQSLRCVD 215 Query: 181 NGFAAVLQQTEPLPLGDGLCWLHSEQLVKRPGLAFVTPAQPLQHQGQLVTGLFCLASLGE 240 F A + P+ LG G H +RP L+ TP + + G+FCLA G+ Sbjct: 216 TDFLASIVGQPPVDLGQGFWLTHHTVGARRPTLSLATPKRATAE----LRGVFCLAGPGD 271 Query: 241 AHQALLERLCDLLLEGRGAELVRATSSRSVLAALGGELPPDWPSARAVLANPHGLHARPA 300 LLER+ L G E ++ S+ ++LA L GE D +A+ L N HGLHARPA Sbjct: 272 ECHDLLERIDTFLA---GDEPIQGLSAEALLARLSGEAA-DAVTAKVTLLNTHGLHARPA 327 Query: 301 QALAQLAKGFAGEIRVRLADSEAAPVSAKSLSKLLALGARRGQTLEFSAEPAIAEDALPA 360 + L Q A+ IR+RL + E A VSA SL++++ LGARRGQTL SA A A+ + Sbjct: 328 KQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLLSATGDDASQAIQS 387 Query: 361 LLAAVREGLGEEVEALAEEALPDAVGEAEEDARPAPLRAGERLQAIAASPGIASGPAHVQ 420 L +A+ GLGE+V L V EAE+ PA L + ++A+AASPG+A PA V Sbjct: 388 LTSAIEGGLGEKVSPLRSADPQTKVPEAEQ--APA-LTDDQPVKAVAASPGLALAPAFVM 444 Query: 421 VAQRFEFQPRGESPAHERERLLRAKRAVDEEIVGLVERSTVKAIREIFVTHREMLDDPEL 480 E+ E + +RL +A + D ++ L+ ++ I H EML D +L Sbjct: 445 RQPTLEYPQFAEDSEQQIQRLNQAVDSADGQLRTLIRQAEGGEAAPILSVHVEMLQDEDL 504 Query: 481 AEQVQLRLNRGESAEAAWSRVVEDSAAQQEALHDALLAERAADLRDLGRRVLARLCGVEA 540 + +N G SAEA W + ++ +A QEAL D LLAERAADLRD+GRRVL+ LCGV Sbjct: 505 YQATLEAINEGASAEAGWWKAIDTAARGQEALADRLLAERAADLRDVGRRVLSNLCGVAM 564 Query: 541 PREPEQPYILVMDEVGPSDVARLDAQRVAGILTARGGATSHSAIIARALGIPALVGAGAA 600 P P+ PYILV D++GPSDVARLD RV G++TARGGATSHSAI+ARALG+PA+VG G Sbjct: 565 PTPPDTPYILVADDLGPSDVARLDTTRVRGLVTARGGATSHSAILARALGLPAVVGTGER 624 Query: 601 VLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAERDARQQRQARADAQRLEPARTRDGHA 660 +L + G+ L++DGE G L P E+ ++ QA A R +PA T DGH Sbjct: 625 ILTILNGSDLVVDGERGCLVPNPGAERCEKIRRRLQQLDALQAEAHENRNQPATTVDGHT 684 Query: 661 VEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMNNARAPDLATQEAEYRRVLDALDGRP 720 +EVCANLG+TA AVE GA+GVGLLRTEF+FM + APDLATQ EY+ DAL+G P Sbjct: 685 IEVCANLGNTAHTPDAVERGADGVGLLRTEFIFMAHPEAPDLATQVTEYQHAFDALNGLP 744 Query: 721 LVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLTLQRPQILETQLRALFRAAGERPLRV 780 LVARTLDVGGDKPL YWP+P E+NP+LG+RGIRL+L RP ILETQ+RAL AAG+RPLR+ Sbjct: 745 LVARTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSLTRPDILETQVRALLTAAGDRPLRI 804 Query: 781 MFPMVGSLDEWRQARDLALRLREEIPLADLQLGIMVEVPSAALLAPVLAREVDFFSVGTN 840 MFPMV L+E+R AR + +++ E+ +++Q+G+M+EVPS ALLA LA EVDFFS+GTN Sbjct: 805 MFPMVKDLEEFRAARAIVTKVQSEVSASNVQVGVMIEVPSCALLASTLAPEVDFFSIGTN 864 Query: 841 DLTQYTLAIDRGHPSLSAQADGLHPAVLQLIDMTVRAAHAEGKWVGVCGELAADPLALPL 900 DLTQYTLAIDRGH LSA++DGLHP+VL+LI MTV AAHA +WVGVCGELA+DP A+P+ Sbjct: 865 DLTQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVEAAHAHNRWVGVCGELASDPQAIPV 924 Query: 901 LVGLGVDELSVSARSIALVKAGVRELQLVAARGLARKALGLASAAEVRALVEA 953 LVGL VDELSV++R + LVKA +R L L AR A KAL LA+A+EVR +EA Sbjct: 925 LVGLDVDELSVTSRRVPLVKACIRGLNLENARQQAEKALSLATASEVRDALEA 977 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: 1809 Number of extensions: 76 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: 956 Length of database: 978 Length adjustment: 44 Effective length of query: 912 Effective length of database: 934 Effective search space: 851808 Effective search space used: 851808 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