Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 380 bits (977), Expect = e-110 Identities = 197/461 (42%), Positives = 299/461 (64%), Gaps = 15/461 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 KL+A+T+CP G+AHT+MAAE LQ+AA R G ++VET+G +G N L + I AD +++ Sbjct: 119 KLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLL 178 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V+ RF GK++ G +++PE + +AL + +A + + ++ ++ Sbjct: 179 AADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVLSGNAVATSASGEKKGEKT 238 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGS-ASFS 180 +Y+H++ GVS+M+P +V GGLLIA++ G E + + + + +IG +F Sbjct: 239 GVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKE-----EGTLAAALMKIGGETAFQ 293 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 M+P+LAGYIAYSIAD+PGL PGMIGG +A T GAGF+GGIIAGF+AGYAA Sbjct: 294 LMVPLLAGYIAYSIADRPGLAPGMIGGLLAGT-------LGAGFIGGIIAGFVAGYAAKA 346 Query: 241 IKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 + + + +P +I+ + PI+IIP+ ASL+ GL ++++G PVA++ A LT +L M S++I Sbjct: 347 VSRWIPLPASIESLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTMGTSNAI 406 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359 LL L+LG M+ D+GGPVNK A+ F ++ +Y M A +PPIG+GIAT + + Sbjct: 407 LLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGIATLIAR 466 Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419 RKF ++RE GKAA +G I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 467 RKFAQTEREAGKAALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMAFGAKLL 526 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459 HGG V ++ A++H L++ +A++AGSLVT + V+K+ Sbjct: 527 APHGGLFVLLIPNAINHALLYLVAILAGSLVTGVIYAVIKQ 567 Score = 59.7 bits (143), Expect = 4e-13 Identities = 29/96 (30%), Positives = 51/96 (53%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 M LL +T+CPNG+ + + + L+ AA RLG S VE + + LT +I AD ++ Sbjct: 1 MNLLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVV 60 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96 + ++ RF+GK++ + + PE ++ A Sbjct: 61 VVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSA 96 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: 811 Number of extensions: 46 Number of successful extensions: 5 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: 579 Length adjustment: 37 Effective length of query: 613 Effective length of database: 542 Effective search space: 332246 Effective search space used: 332246 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