Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 7025094 Shewana3_2257 phosphoenolpyruvate--protein phosphotransferase (RefSeq)
Query= TCDB::Q9HY55 (956 letters) >FitnessBrowser__ANA3:7025094 Length = 567 Score = 323 bits (829), Expect = 1e-92 Identities = 206/561 (36%), Positives = 314/561 (55%), Gaps = 12/561 (2%) Query: 403 LQAIAASPGIASGPA-HV-QVAQRFEFQPRGESPAHERE-RLLRAKRAVDEEIVGLVERS 459 + I S GIA G A H+ Q +++P S +++ + ++A +A+ +++ + Sbjct: 3 ITGIIVSSGIAFGQALHLTQAEHHLDYRPIPLSRIPQQQSKFVKALQALQQQLSHSQTKL 62 Query: 460 TVKAIR-EIFVTHREMLDDPELAEQVQLRLNRGE-SAEAAWSRVVEDSAAQQEALHDALL 517 ++ ++ +L+D EL +QV+ + + SA A R+ A + E+L D L Sbjct: 63 DPQSENYQLIEADLLLLEDEELIDQVKEAIRTLQLSASVAVERIFAHQANELESLDDPYL 122 Query: 518 AERAADLRDLGRRVLARLCGV--EAPREPEQPYILVMDEVGPSDVARLDAQRVAGILTAR 575 A RA D+R LG+R++ + G + + +P IL+ ++ P++ A L ++++GI+ Sbjct: 123 ANRAQDVRCLGQRLVTAINGRLDQGLAQLTEPTILLAQDLTPAEFALLPKEQLSGIVLKT 182 Query: 576 GGATSHSAIIARALGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAER 635 GG TSH+AI+ARA GIPA++ + GT L+LD G L V P+ E + Sbjct: 183 GGLTSHTAILARAAGIPAILSCQFDAEFIPNGTPLVLDALSGELFVNPAPELQARLTVTL 242 Query: 636 DARQQRQARADAQRLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFMN 695 Q R+A A R PA+T+DGH V + AN+G+ ++GA+G+GL RTEF+ M+ Sbjct: 243 HHEQARRAALQAYRDVPAKTQDGHLVGLMANVGNLNDITHVGDVGADGIGLFRTEFMLMH 302 Query: 696 NARAPDLATQEAEYRRVLDALDGRPLVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRLT 755 + PD Q Y L AL G+ RTLD+G DK LP E+NP LGLRG+R T Sbjct: 303 TSTLPDEKAQYNLYCEALHALGGKTFTIRTLDIGADKELPCLCQEVEDNPALGLRGVRYT 362 Query: 756 LQRPQILETQLRALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLADL 810 L P++ +TQLRA+ RAA P+R+MFPMV ++E Q L + EE +L Sbjct: 363 LAHPELFKTQLRAILRAANHGPIRLMFPMVNQVEELDQIFALIAECQDALEEEEKGFGEL 422 Query: 811 QLGIMVEVPSAALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQL 870 GI+VE P+A + + +DF S+GTNDLTQY +A DR +P L+ L PA+L L Sbjct: 423 SYGIVVETPAAVMNLASMLPRLDFVSIGTNDLTQYAMAADRTNPQLTRDYPSLSPAILGL 482 Query: 871 IDMTVRAAHAEGKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLVA 930 I MTV A A G V +CGELA+ PL +PLL+G+G+DELSV+ ++ VKA V + QL Sbjct: 483 IKMTVDQAKAAGVKVSLCGELASSPLMVPLLIGMGLDELSVNLSALLEVKAAVCQGQLTK 542 Query: 931 ARGLARKALGLASAAEVRALV 951 LA A+ +E++ + Sbjct: 543 FSALAHTAMQQNRISELQQCI 563 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: 955 Number of extensions: 41 Number of successful extensions: 2 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: 567 Length adjustment: 40 Effective length of query: 916 Effective length of database: 527 Effective search space: 482732 Effective search space used: 482732 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