Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 259 bits (663), Expect = 1e-73 Identities = 156/465 (33%), Positives = 248/465 (53%), Gaps = 39/465 (8%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQA--------GTAVFDHLPLIFA 55 F Q+L ++ ++PIA+LPA G++L L V IPF+ + G +F +P++FA Sbjct: 27 FAQRLSQALLIPIAILPAAGVMLGL---TVSPIPFMPEVLNVLMLAVGKLIFAIMPILFA 83 Query: 56 IGIAIGISKDSNGAAGLSGAISYLMLDAATKTID-------------KTNNMAVFGGIIA 102 + +AIG +D G A + Y ++ A + +T + + GG++ Sbjct: 84 VAVAIGFCRDQ-GIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLI 142 Query: 103 GLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGE 162 G + + + +LP FF GRR +L + + L + +WP + I + Sbjct: 143 GGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSD 202 Query: 163 WML-GLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYN-----GVTGDLARFFAKD 216 W + I G++G RLLIPLGLHH+ N F+ + G+Y V G++AR+ A D Sbjct: 203 WAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGD 262 Query: 217 PTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFA 276 P AG G+ I M+GLPAA LA+ A S+R AG+M+ A +++TG+TEPIEFA Sbjct: 263 PQAGNLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFA 321 Query: 277 FMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGIC 336 FMF++PLL+ +H +L+GL+ F+ L I FS G +D+ L + ++ ++G Sbjct: 322 FMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPL 381 Query: 337 YAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDH 396 A +Y+I+F I A NLKTPGR D + E+ ++ LGG++N+ ++ Sbjct: 382 TAVIYYILFRGSILAFNLKTPGRLQSDGTKGSKESL------RAIIAALGGRDNIVELNA 435 Query: 397 CATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441 C TRLRL+V LV++ L + GAKGV+ G+ VQ++ G E Sbjct: 436 CLTRLRLSVHSPELVNKVRLSQLGAKGVIVM-GKGVQIVYGTKAE 479 Lambda K H 0.326 0.144 0.429 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: 554 Number of extensions: 33 Number of successful extensions: 7 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: 452 Length of database: 499 Length adjustment: 33 Effective length of query: 419 Effective length of database: 466 Effective search space: 195254 Effective search space used: 195254 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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