Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337 Length = 575 Score = 382 bits (980), Expect = e-110 Identities = 204/463 (44%), Positives = 301/463 (65%), Gaps = 22/463 (4%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +L+AIT+CP G+AHT+MAAE LQ+AA +LG ++VETQG +G N L+ E I EAD +++ Sbjct: 117 RLVAITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLL 176 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 A D V +RF GKK+ +++ E + KAL + + + S + + ++ Sbjct: 177 ATDIEVATERFAGKKIYRCSTGIALKQAEATLNKAL---VEGRQESASSGASAPAKSEKT 233 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGE--KTPKGLVIPDDSFWKTIEQIGS-AS 178 +Y+HL+ GVSFM+P +V GGL+IA++ G E K P L + QIG + Sbjct: 234 GVYKHLLTGVSFMLPMVVAGGLMIALSFVFGIEAFKEPGTLAA-------ALMQIGGDTA 286 Query: 179 FSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAA 238 F M+P+LAGYIAYSIAD+PGL PGMIGG +A+T GAGF+GGIIAGFLAGYAA Sbjct: 287 FKLMVPLLAGYIAYSIADRPGLAPGMIGGMLAST-------LGAGFIGGIIAGFLAGYAA 339 Query: 239 LWIKKL-KVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSS 297 I + ++P++++ + PI+IIP+ ASL GL ++++G PVA + +LT +L M ++ Sbjct: 340 KAISRYARLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTN 399 Query: 298 SILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFL 357 +ILL ++LGAM+ D+GGP+NK A+ F ++ +Y M A +PPIGLGIATF+ Sbjct: 400 AILLGVLLGAMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFI 459 Query: 358 GKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVG 417 +RKF ++RE GKAA +GL I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 460 ARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCK 519 Query: 418 DRVAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459 HGG V ++ A++H L++ +A++AGSL+T + +LK+ Sbjct: 520 LMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTGVAYALLKR 562 Score = 49.7 bits (117), Expect = 4e-10 Identities = 24/72 (33%), Positives = 39/72 (54%) Query: 6 ITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIIIAADR 65 +T+CPNG+ + + A L AA R G S VE E +L+ + A+ +++ A Sbjct: 1 VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60 Query: 66 SVNKDRFIGKKL 77 V+ RF+GK+L Sbjct: 61 PVDMSRFVGKRL 72 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: 763 Number of extensions: 46 Number of successful extensions: 7 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: 575 Length adjustment: 37 Effective length of query: 613 Effective length of database: 538 Effective search space: 329794 Effective search space used: 329794 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