Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 385 bits (988), Expect = e-111 Identities = 204/461 (44%), Positives = 297/461 (64%), Gaps = 16/461 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +++A+T+CP G+AHT+MAAE LQ+AA +LG + VETQG +G N L+ E I AD +++ Sbjct: 119 RIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQGSVGARNPLSAEAIAAADVVLL 178 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V RF GK++ G +++ + KAL V A + + + ++ Sbjct: 179 AADIEVPTARFAGKRIYRCGTGIALKQARATLDKAL-AQATVENGADAAAATTPTKSEKT 237 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGS-ASFS 180 +Y+HL+ GVSFM+P +V GGLLIA++ G E + +P + QIG A+F Sbjct: 238 GVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAYKEAGTLP-----AALMQIGGEAAFK 292 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 M+P+LAGYIA+SIAD+PGL PGMIGG +A+T GAGF+GGI+AGFLAGY+A Sbjct: 293 LMVPLLAGYIAWSIADRPGLAPGMIGGLLAST-------LGAGFIGGIVAGFLAGYSAKA 345 Query: 241 IKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 I + ++P +++ + PI+IIP+ ASL GL ++++G PVA + LT +L M +++I Sbjct: 346 IARWARLPSSLEALKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHFLDSMGTTNAI 405 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359 LL L+LG M+ D+GGP+NK A+ F ++ +Y M A +PPIGLGIATFL + Sbjct: 406 LLGLLLGGMMCVDLGGPINKAAYAFSVGLLASSSYAPMAATMAAGMVPPIGLGIATFLAR 465 Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419 RKF S+RE GKAA +GL I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 466 RKFAQSEREAGKAALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLM 525 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459 HGG V ++ A++H L++ +A++AGSLVTA+ V+KK Sbjct: 526 APHGGLFVLLIPNAINHALLYLLAIVAGSLVTAVVYAVIKK 566 Score = 55.1 bits (131), Expect = 9e-12 Identities = 30/96 (31%), Positives = 49/96 (51%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 M + +T+CPNG + ++A L AA R G S VE Q E +L+ +I EAD ++ Sbjct: 1 MNIAIVTACPNGQVSSVLSARLLSAAAQRRGWSTSVEVQNTEHPERQLSAAQIAEADWVL 60 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96 + + V+ RF+GK+L + E + +A Sbjct: 61 VVSTGPVDLARFVGKRLYQSTPSQALADREGFLDEA 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: 764 Number of extensions: 51 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 650 Length of database: 580 Length adjustment: 37 Effective length of query: 613 Effective length of database: 543 Effective search space: 332859 Effective search space used: 332859 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