Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate BWI76_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Koxy:BWI76_RS27570 Length = 363 Score = 229 bits (583), Expect = 2e-64 Identities = 135/345 (39%), Positives = 200/345 (57%), Gaps = 22/345 (6%) Query: 123 IYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKT-PKGLVIPDDSFWKTIEQIGSASFSF 181 I +HL+ G+S+M+P IV G+ IA+ LGG K IP W + QIG Sbjct: 12 IKKHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKTGTIP----WM-LNQIGGWGMGL 66 Query: 182 MIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALWI 241 ++P++ IAYSIAD+PG PG+I G++ G + GF+GG++ GFL GY L + Sbjct: 67 IVPLICAAIAYSIADRPGFAPGLIVGFVC--GQIH-----TGFIGGMLGGFLVGYTVLAL 119 Query: 242 KK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSIL 300 K +++PK++Q +MPI+++PV +++I GL + LIG P+A + +L L M+G S L Sbjct: 120 KHYIRLPKSMQGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQGGSRFL 179 Query: 301 LALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAI---CIPPIGLGIATFL 357 L ILGAM +FD GGPVNK LF ++ G Y GP AV IPP G+ ++ L Sbjct: 180 LGAILGAMATFDFGGPVNKTMSLFADGLLVSGVY---GPEAVKFVGSIIPPFGITLSFLL 236 Query: 358 GKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVG 417 + K+ ++RE KAAF MG+ ITEG IP AA+D LRV+ S + S + M V Sbjct: 237 TRHKYTRAEREALKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTWGVE 296 Query: 418 DRVAHGGPIVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLKKDIT 462 V HGG V L H L+F +++ G+++ + +++ KK +T Sbjct: 297 SPVPHGGMFVVPL--FTHPLLFCLSLAIGTVICGVMLSLWKKPVT 339 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: 544 Number of extensions: 30 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: 650 Length of database: 363 Length adjustment: 34 Effective length of query: 616 Effective length of database: 329 Effective search space: 202664 Effective search space used: 202664 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