Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_106714139.1 CU102_RS26935 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >NCBI__GCF_003010955.1:WP_106714139.1 Length = 661 Score = 373 bits (958), Expect = e-107 Identities = 247/661 (37%), Positives = 354/661 (53%), Gaps = 24/661 (3%) Query: 286 RIALANAH-GLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQV 344 R + H GLHARPA +LAKSFE +I + D +V+ KS KL+ LG + Sbjct: 3 RSTIVRVHDGLHARPATRFVKLAKSFESDIELVKAD---RSVNAKSSVKLMLLGVKENDE 59 Query: 345 LELIAEPSIAADALPALLRAIEE---GLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCV 401 + + A + A +A+ AL+ +E G+ ED A+ +V V P S Sbjct: 60 ITVRATGADAIEAVEALIGYLENPNSGILEDGAAEAAKPAEKKVPLGPESSSVGPGSAGK 119 Query: 402 IQAVAAAPGIAIG------PAHIQVLQAIDYPLRGESTAIERERLKTSLADVR-RDIEGL 454 ++ V A+ G+AIG PA I+ + L G+ E RLK + A V+ R + L Sbjct: 120 LRGVPASEGVAIGLAFGFFPAEIKHENRL---LNGDEIPGEVARLKQAFAAVQDRMDKSL 176 Query: 455 IQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDA 514 + A++ R I +++ D ELT V + G A +A + A S+ D Sbjct: 177 AATNLAESDRGIIAALKDIAGDDELTGAVAALVDGGIDAVSAVIGATSKIAADFASMDDP 236 Query: 515 LLAERAADLRDIGRRVLAQLCGIETPSEPDQPY--ILVMDEVGPSDVARLDPTRVAGILT 572 L RA D+ +GR++ L G + + P IL+ +++G D+AR R+AG++ Sbjct: 237 YLNARADDVNAVGRQICLALLGQDDANLDAIPAGAILIAEDIGAWDLARAPLKRIAGVIC 296 Query: 573 ARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAE 632 GGAT+H AI+ARA GIPA++G G +V L + LDG G + + D AT R + Sbjct: 297 GHGGATSHVAIIARAHGIPAVLGVGRSVQDLQHVNTVALDGNSGDIFPEPDQATADRFHK 356 Query: 633 ERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIF 692 + E QA A R DG +E+ AN+G + +A + GA G+GL RTEL+F Sbjct: 357 QIGKAESDKQALKAYRDVTPKRADGTVIEIAANLGSLEEIEAAQDAGAMGVGLFRTELLF 416 Query: 693 MAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIR 752 M H P E Q Y + A P++VRTLD+GGDKP+ EENPFLG RGIR Sbjct: 417 MRHIHLPSEDLQAETYATLAKAFAPYPVIVRTLDIGGDKPISGIDFPAEENPFLGWRGIR 476 Query: 753 LTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVA 807 + L RP + + QLRALLRAA + +++M PMV +DE R AR + E E+ A Sbjct: 477 MCLDRPDVFKPQLRALLRAATHGNIKVMLPMVSGLDEVRAARVLIEECADELKREGKAYA 536 Query: 808 DLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVL 867 LG+M+E P+A ++AP+LA+EV FFS+GTNDLTQY +A DR +PT++ D HPAV+ Sbjct: 537 AFDLGVMVETPAAVMIAPMLAREVAFFSIGTNDLTQYIMAADRLNPTVAKLNDVTHPAVM 596 Query: 868 QLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSL 927 I++T +A G VG+CGE A P +P V +G+ ELS+S SI K V +L Sbjct: 597 AAIELTAKAGVEAGIMVGMCGEAAGRPDLIPSFVKMGLTELSMSPSSIPRAKKCVLDLET 656 Query: 928 A 928 A Sbjct: 657 A 657 Lambda K H 0.319 0.135 0.383 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: 1208 Number of extensions: 56 Number of successful extensions: 3 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: 661 Length adjustment: 41 Effective length of query: 912 Effective length of database: 620 Effective search space: 565440 Effective search space used: 565440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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