Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate 17988 b3949 predicted enzyme IIC component of PTS (NCBI)
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Keio:17988 Length = 359 Score = 285 bits (729), Expect = 2e-81 Identities = 157/337 (46%), Positives = 217/337 (64%), Gaps = 17/337 (5%) Query: 125 RHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPD---DSFWKTIEQIGSASFSF 181 +HLM GVS M+PF+V GG+L+AV++ L G KG V PD D K + IG A + Sbjct: 13 QHLMTGVSHMIPFVVSGGILLAVSVMLYG----KGAV-PDAVADPNLKKLFDIGVAGLTL 67 Query: 182 MIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALWI 241 M+P LA YI YSIA++ L P IG ++ ++ GAGF G +IAG + G ++ Sbjct: 68 MVPFLAAYIGYSIAERSALAPCAIGAWVG-------NSFGAGFFGALIAGIIGGIVVHYL 120 Query: 242 KKLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSILL 301 KK+ V K ++ +MPI IIP+ +LI ++ +G PV + SLT WL GM+ S ++L Sbjct: 121 KKIPVHKVLRSVMPIFIIPIVGTLITAGIMMWGLGEPVGALTNSLTQWLQGMQQGSIVML 180 Query: 302 ALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGKRK 361 A+I+G M++FDMGGPVNKVA+ F + +G Y ++ AV ICIPP+G+G+AT +G++ Sbjct: 181 AVIMGLMLAFDMGGPVNKVAYAFMLICVAQGVYTVVAIAAVGICIPPLGMGLATLIGRKN 240 Query: 362 FEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDRVA 421 F A +RE GKAA MG G+TEGAIPFAA DPLRVIPSIM GS+ G+V A + VG + Sbjct: 241 FSAEERETGKAALVMGCVGVTEGAIPFAAADPLRVIPSIMVGSVCGAVTAAL--VGAQCY 298 Query: 422 HGGPIVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLK 458 G + VL V+ L + AV G++VTA+ VNVLK Sbjct: 299 AGWGGLIVLPVVEGKLGYIAAVAVGAVVTAVCVNVLK 335 Lambda K H 0.319 0.137 0.386 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: 569 Number of extensions: 31 Number of successful extensions: 6 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: 650 Length of database: 359 Length adjustment: 34 Effective length of query: 616 Effective length of database: 325 Effective search space: 200200 Effective search space used: 200200 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: 52 (24.6 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