Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_086509379.1 BZY95_RS07790 PTS system fructose-like transporter subunit IIB
Query= BRENDA::O31645 (650 letters) >NCBI__GCF_002151265.1:WP_086509379.1 Length = 580 Score = 396 bits (1017), Expect = e-114 Identities = 212/468 (45%), Positives = 305/468 (65%), Gaps = 18/468 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 K++A+T+CP G+AHT+MAAE L +A LG I+VETQG +G +NKLT+EEI AD +I+ Sbjct: 122 KIVAVTACPTGVAHTFMAAEALSEAGKSLGHEIRVETQGSVGAQNKLTDEEIAAADVVIL 181 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 A D V+ RF GK++ + ++KP I+ AL+ V S T S + K+ Sbjct: 182 ACDIEVDPTRFAGKRIYRTSTGNALKKPRPTIEAALD-QAEVEDSGTARRSDASRSIKEK 240 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSAS-FS 180 +Y+HL+ GVSFM+P +V GGLLIA++ G E + + + + QIG + F+ Sbjct: 241 GVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQE-----EGTLAAALMQIGGGTAFA 295 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 MIP+LAGYIAYSIAD+PG+ PGMIGG +AA AGF+GGIIAGFLAGY AL Sbjct: 296 LMIPVLAGYIAYSIADRPGIAPGMIGGMLAANIE-------AGFIGGIIAGFLAGYVALA 348 Query: 241 IKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 + + +K+P +++ + PI+IIP+ +SL+ GL +++IG PVA I A LT +LAGM ++++ Sbjct: 349 VTRHVKLPASVESLKPILIIPLVSSLVTGLTMIYIIGEPVAAILAGLTGFLAGMDATNAV 408 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359 LL ++LGAM+ FD+GGPVNK A+ FG ++ Y M I A +P IG+GIA+F+ + Sbjct: 409 LLGILLGAMMCFDLGGPVNKAAYTFGVGLLASQTYAPMAAIMAAGMVPAIGMGIASFVAR 468 Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419 KF +RE GKA+F +GL I+EGAIPFAA+DPLRVIP+ +AG ++M+ Sbjct: 469 HKFSEPEREAGKASFVLGLCFISEGAIPFAAKDPLRVIPACIAGGAVTGALSMLVGAQLM 528 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKKDITASPV 466 HGG V ++ A+ VL++ A++ GSLVT L +K+ A+PV Sbjct: 529 APHGGIFVLLIPNAITPVLLYLGAIVIGSLVTGLGYAAIKRG--AAPV 574 Score = 68.6 bits (166), Expect = 8e-16 Identities = 31/96 (32%), Positives = 57/96 (59%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 M ++ +T+CP+G+A T++AA L++AA RLG +E + ++ + I A+ I+ Sbjct: 1 MNVIIVTACPSGMATTFLAARRLEQAARRLGWQASIEMHSQLEAVEPVSADAIAAAELIV 60 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96 +AAD+ +RF GK+L + + + PE +Q+A Sbjct: 61 VAADQIPAAERFAGKQLFRAAIGEALPDPEAFLQRA 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: 859 Number of extensions: 53 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: 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 24 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