Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate Pf1N1B4_1144 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__pseudo1_N1B4:Pf1N1B4_1144 Length = 579 Score = 384 bits (987), Expect = e-111 Identities = 207/469 (44%), Positives = 304/469 (64%), Gaps = 18/469 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +L+A+T+CP G+AHT+MAAE LQ+AA RLG ++VETQG +G N L+ E I +AD +++ Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLL 180 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V +RF GKK+ G +++ E + KAL SA+ G +++K Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKALAEG--KQESASTGAKGPAKQEKTG 238 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGS-ASFS 180 IY+HL+ GVSFM+P +V GGL+IA++ G + + + + QIG +F Sbjct: 239 -IYKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKE-----EGTLAAALMQIGGDTAFK 292 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 M+P+LAGYIAYSIAD+PGL PGMIGG +A+T GAGF+GGIIAGF+AGYAA Sbjct: 293 LMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-------LGAGFIGGIIAGFIAGYAAQA 345 Query: 241 IKKL-KVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 I + ++P++++ + PI+IIP+ ASL GL ++++G PVA + A LT +L M +++I Sbjct: 346 INRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTHFLDSMGTTNAI 405 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359 LL ++LG M+ D+GGP+NK A+ F ++ +Y M A +PPIGLGIATF+ + Sbjct: 406 LLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIAR 465 Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419 RKF ++RE GKAA +GL I+EGAIPFAA+DPLRVIP+ +AG ++M Sbjct: 466 RKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLM 525 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKKDITASPVL 467 HGG V ++ A++H L++ +A++AGSL+TA+ +LK+ T L Sbjct: 526 APHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVTYALLKRPETVELAL 574 Score = 53.5 bits (127), Expect = 3e-11 Identities = 27/97 (27%), Positives = 49/97 (50%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 MKL +T+CPNG+ + + A L AA R G S VE E +L+ I A+ ++ Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVL 60 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL 97 + V+ RF+GK++ ++ E ++++ + Sbjct: 61 LVTSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGV 97 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: 776 Number of extensions: 49 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: 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