Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 377 bits (969), Expect = e-109 Identities = 207/462 (44%), Positives = 297/462 (64%), Gaps = 18/462 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +++A+T+CP G+AHT+MAAE L AA G I+VETQG +G ++ LTEEEI AD +I+ Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 A D V+ RF GK++ ++KP + I+ AL + + K+ + +K+ Sbjct: 188 ACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGASGSGEKKG 247 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSAS-FS 180 P Y+HL+ GVSFM+P +V GGLLIA++ G E + + + + QIG + F Sbjct: 248 P-YKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQE-----EGTLAAALMQIGGGTAFK 301 Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240 MIP+LAGYIA+SIAD+PGL PGMIGG++A GAGFLGGI+AGFLAGY A + Sbjct: 302 LMIPLLAGYIAWSIADRPGLAPGMIGGFLAGE-------LGAGFLGGIVAGFLAGYVARF 354 Query: 241 I-KKLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299 I +KL +P++I+ + PI+IIP+ ASL+ GL +++IG P+A I +LT +L GM +++I Sbjct: 355 ISQKLPMPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTNAI 414 Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMI--GEGNYEIMGPIAVAICIPPIGLGIATFL 357 LL ILGAM+ FD+GGPVNK A+ FG ++ G G M I A +P IG+G+A+F+ Sbjct: 415 LLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVASFI 474 Query: 358 GKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVG 417 +RKF ++R+ G+A+F +GL I+EGAIPF A+DPLRVIP M G ++M+ V Sbjct: 475 ARRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFTVK 534 Query: 418 DRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLK 458 HGG ++A+ AV VL + IA+ GSLV +LK Sbjct: 535 LMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576 Score = 72.0 bits (175), Expect = 7e-17 Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 1/97 (1%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIG-VENKLTEEEIREADAI 59 M L+ +T+CP G+A ++AA L++AA+R G S+ +T+G G +NK +E I++AD + Sbjct: 1 MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60 Query: 60 IIAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96 I A VN D + GK+LL + V + P+ ++ +A Sbjct: 61 IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRA 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: 884 Number of extensions: 58 Number of successful extensions: 9 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: 587 Length adjustment: 37 Effective length of query: 613 Effective length of database: 550 Effective search space: 337150 Effective search space used: 337150 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