Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 252 bits (643), Expect = 2e-71 Identities = 153/450 (34%), Positives = 238/450 (52%), Gaps = 39/450 (8%) Query: 19 LPAVGIILALGREDVFNIPFVYQA--------GTAVFDHLPLIFAIGIAIGISKDSNGAA 70 +PA G++L L V IPF+ + G +F +P++FA+ +AIG +D G A Sbjct: 1 MPAAGVMLGL---TVSPIPFMPEVLTVLMLAVGKLIFAIMPILFAVAVAIGFCRDQ-GIA 56 Query: 71 GLSGAISYLMLDAATKTID-------------KTNNMAVFGGIIAGLIAGYTYNRFKDTK 117 + Y ++ A + +T + + GG++ G + + + + Sbjct: 57 AFTAVFGYGVMTATLAALADLYQLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQYIR 116 Query: 118 LPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWML-GLGGIGAGIFG 176 LP FF GRR +L + + L I VWPP+ I +W + I G++G Sbjct: 117 LPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYG 176 Query: 177 LFNRLLIPLGLHHVLNNIFWFQFGEYN-----GVTGDLARFFAKDPTAGTYMTGFFPIMM 231 RLLIPLGLHH+ N F+ + G+Y V G++AR+ A DP AG G+ I M Sbjct: 177 ALERLLIPLGLHHIWNAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGNLAGGYL-IKM 235 Query: 232 FGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVL 291 +GLPAA LA+ A+PS+R AG+M+ A +++TG+TEPIEFAFMF++P L+ +H +L Sbjct: 236 WGLPAAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLL 295 Query: 292 TGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKA 351 +GL+ F+ L I FS G +D+ L + ++ + +G A +Y+++F I A Sbjct: 296 SGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVFLGPLTAVIYYLLFRGSILA 355 Query: 352 LNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALV 411 NLKTPGR + D E+ ++ LGG+EN+ ++ C TRLRL+V LV Sbjct: 356 FNLKTPGRLEPDEPHGAKESL------RAIIAALGGRENIVELNACLTRLRLSVHSPELV 409 Query: 412 DEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441 ++ L + GAKGV+ G+ VQV+ G E Sbjct: 410 NKVRLSQLGAKGVIVM-GKGVQVVYGTKAE 438 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: 518 Number of extensions: 30 Number of successful extensions: 6 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: 452 Length adjustment: 33 Effective length of query: 419 Effective length of database: 419 Effective search space: 175561 Effective search space used: 175561 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