Align Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 201387 SO2237 phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file)
Query= TCDB::Q9HY55 (956 letters) >FitnessBrowser__MR1:201387 Length = 567 Score = 319 bits (817), Expect = 4e-91 Identities = 203/550 (36%), Positives = 297/550 (54%), Gaps = 14/550 (2%) Query: 403 LQAIAASPGIASGPA----HVQVAQRFEFQPRGESPAHERERLLRAKRAVDEEI-VGLVE 457 + I S GIA G A H + + P P ++ + L+A +A+ +++ + + Sbjct: 3 ITGIIVSSGIAFGKALHLNHCENHLDYRPIPLSRIPL-QQSKFLKALQALKQQLSLSQAK 61 Query: 458 RSTVKAIREIFVTHREMLDDPELAEQVQLRLNRGE-SAEAAWSRVVEDSAAQQEALHDAL 516 ++ +LDD EL EQV+ + + SA A R+ A + E+L D Sbjct: 62 LDPESENYQLIEADLLLLDDDELIEQVKEAIRTLQLSASVAVERIFAHQANELESLDDPY 121 Query: 517 LAERAADLRDLGRRVLARLCG--VEAPREPEQPYILVMDEVGPSDVARLDAQRVAGILTA 574 LA RA D+R LG+R++ + G + + + IL+ ++ P++ A L + ++GI+ Sbjct: 122 LANRAQDVRCLGQRIVTAINGRLEQGLADLSEATILLAQDLTPAEFALLPKEHISGIVLK 181 Query: 575 RGGATSHSAIIARALGIPALVGAGAAVLGLEPGTALLLDGEHGWLQVAPSTEQLQQAAAE 634 GG TSH+AI+ARA GIPA++ + T L+LD G L V P EQ + Sbjct: 182 TGGLTSHTAILARAAGIPAMLSCQFDAEFIPNNTPLVLDALSGVLYVNPEPEQQARLTVT 241 Query: 635 RDARQQRQARADAQRLEPARTRDGHAVEVCANLGDTAGAARAVELGAEGVGLLRTEFVFM 694 Q R+ R PA+T+DGH V + AN+G+ + GA+G+GL RTEF+ M Sbjct: 242 LHHEQARRQALQTYRDVPAQTQDGHHVGLLANVGNLNEITHVKDEGADGIGLFRTEFMLM 301 Query: 695 NNARAPDLATQEAEYRRVLDALDGRPLVARTLDVGGDKPLPYWPIPHEENPYLGLRGIRL 754 N + PD Q Y L ALDG+ RTLD+G DK LP E+NP LG RG+R Sbjct: 302 NTSTLPDEKAQYNLYCEALHALDGKTFTIRTLDIGADKELPCLCQNIEDNPALGQRGVRY 361 Query: 755 TLQRPQILETQLRALFRAAGERPLRVMFPMVGSLDEWRQARDLALRLR-----EEIPLAD 809 TL P++ +TQLRA+ RAA P+R+MFPMV ++E + L + EE + Sbjct: 362 TLAHPELFKTQLRAILRAANHGPIRLMFPMVNQVEELDEIFKLIAECQDALEEEEKGYGE 421 Query: 810 LQLGIMVEVPSAALLAPVLAREVDFFSVGTNDLTQYTLAIDRGHPSLSAQADGLHPAVLQ 869 L GI+VE P+A L + +DF S+GTNDLTQY +A DR +P L+ L PA+L Sbjct: 422 LSYGIVVETPAAVLNLASMLPRLDFVSIGTNDLTQYAMAADRTNPQLTKDYPSLSPAILH 481 Query: 870 LIDMTVRAAHAEGKWVGVCGELAADPLALPLLVGLGVDELSVSARSIALVKAGVRELQLV 929 LI+MT+ A A G V +CGELA+ P PLLVG+G+DELSV+ S+ VKA + + +L Sbjct: 482 LINMTITQAKATGVTVSLCGELASSPQMAPLLVGMGLDELSVNLSSLLEVKAAICQGELA 541 Query: 930 AARGLARKAL 939 LA A+ Sbjct: 542 KFSELAHTAM 551 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: 892 Number of extensions: 31 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