Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate GFF782 PS417_03975 FruA
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__WCS417:GFF782 Length = 569 Score = 375 bits (963), Expect = e-108 Identities = 200/472 (42%), Positives = 300/472 (63%), Gaps = 25/472 (5%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +++AIT+CP G+AHT+MAAE LQ+ A RLG ++VETQG +G L+ + I EAD +++ Sbjct: 115 RIVAITACPTGVAHTFMAAEALQQTAKRLGYDLQVETQGSVGARTPLSPQAIAEADVVLL 174 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V +RF GKK+ G +++ E + KAL + + SG +K++ Sbjct: 175 AADIEVATERFAGKKIYRCGTGIALKQSEATLNKAL-----AEGAVESAASGAVAKKEKT 229 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEK-TPKGLVIPDDSFWKTIEQIGSASFS 180 +Y+HL+ GVSFM+P +V GGLLIA++ G KG + ++ +G +F Sbjct: 230 GVYKHLLTGVSFMLPMVVAGGLLIALSFMFGITAFEEKGTLAA------ALKTVGDQAFM 283 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 M+P+LAGYIAYSIAD+P L PGMIGG +A T GAGF+GGI AGFLAGY Sbjct: 284 LMVPLLAGYIAYSIADRPALAPGMIGGLLATT-------LGAGFIGGIFAGFLAGYCVKL 336 Query: 241 IKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 I + +++P+++ + PI+IIP+ ASL GLA ++L+G PVA++ LT +L M ++++ Sbjct: 337 ITRAVQLPQSLDALKPILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNTMGTTNAV 396 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359 LL ++LG M+ D+GGP+NK A+ F M+ + + A +PPIG+GIATFL + Sbjct: 397 LLGILLGGMMCVDLGGPINKAAYAFSVGMLAAHSGAPIAATMAAGMVPPIGMGIATFLAR 456 Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419 RKF ++RE GKAA +G+ I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 457 RKFAQTEREAGKAAIILGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLA 516 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK----DITASPV 466 HGG V V+ A++H L++ +A++AGSL+T L ++K+ ++T +PV Sbjct: 517 APHGGLAVLVIPNAMNHALLYLLAIVAGSLLTGLVYALIKRPEAQELTVAPV 568 Score = 52.0 bits (123), Expect = 7e-11 Identities = 26/77 (33%), Positives = 44/77 (57%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 MKL +T+CPNG+ + + A L AA R G S VE E +L++ I +A+ ++ Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDVQRPERQLSQATIDDAEWVL 60 Query: 61 IAADRSVNKDRFIGKKL 77 + + V+ RF+GK++ Sbjct: 61 LVSSTPVDMQRFVGKRV 77 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: 769 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 650 Length of database: 569 Length adjustment: 37 Effective length of query: 613 Effective length of database: 532 Effective search space: 326116 Effective search space used: 326116 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: 53 (25.0 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