Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_108222994.1 C8J29_RS00715 PTS fructose transporter subunit EIIBC
Query= BRENDA::O31645 (650 letters) >NCBI__GCF_003046325.1:WP_108222994.1 Length = 581 Score = 387 bits (995), Expect = e-112 Identities = 211/468 (45%), Positives = 303/468 (64%), Gaps = 22/468 (4%) Query: 1 MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60 +K++AITSCP GIAHT+MAAE L + A G I+VETQG +G +++LT EI AD +I Sbjct: 119 LKIVAITSCPTGIAHTFMAAEGLVEGARAQGHQIRVETQGSVGAQDELTAAEIAAADLVI 178 Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQ 120 IAAD+ V+ RF GK+L + I LI+KA + + + SE+ + KK Sbjct: 179 IAADKQVDLGRFGGKRLFLSPTKPAITDGAGLIRKA-QAEARMQAGSASSEAAQPEAKKV 237 Query: 121 NPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSF----WKTIEQIGS 176 +Y+HLM GVSFM+PF+V GGLLIA+A LGG + + +D + T+ QIG+ Sbjct: 238 G-VYKHLMTGVSFMLPFVVAGGLLIAIAFALGG------IYVYEDQYAGTLGHTLFQIGA 290 Query: 177 -ASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAG 235 +F+ M+P LAGYIA+SIAD+PGL PGM GG IA T GAGFLGGI+AGF+AG Sbjct: 291 KGAFTLMVPALAGYIAWSIADRPGLAPGMTGGVIAGT-------IGAGFLGGIVAGFIAG 343 Query: 236 YAALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMK 294 Y LW+ + +K+PK +Q + P++I+P+ + + GL +++G P A++ A++T +L GM+ Sbjct: 344 YGVLWLNRAIKLPKTLQGLKPVLILPLLGTALTGLLMYYVVGEPTARLLATITAFLQGMQ 403 Query: 295 GSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIA 354 G+S+ LL L+LG M++ DMGGPVNK A+ F + +I E M + A +PPI L +A Sbjct: 404 GTSAALLGLLLGGMMAVDMGGPVNKAAYAFATTLIAANVLEPMAAVMCAGMVPPIALAVA 463 Query: 355 TFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIG 414 L +F +RE G AAF +GL +TEGAIPFAA+DPLRVIPS++AGS I M Sbjct: 464 CRLLPARFTPEEREAGNAAFVLGLAFVTEGAIPFAARDPLRVIPSLIAGSAVAGAICMAL 523 Query: 415 NVGDRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLKKDI 461 V RV HGG ++ + AV ++ F IA++AG+ V+ L + ++K+ + Sbjct: 524 GVAQRVPHGGVFVLPIPNAVTNLTGFGIALVAGTAVSVLALALVKRRV 571 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: 851 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 650 Length of database: 581 Length adjustment: 37 Effective length of query: 613 Effective length of database: 544 Effective search space: 333472 Effective search space used: 333472 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