Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Koxy:BWI76_RS11130 Length = 477 Score = 366 bits (939), Expect = e-105 Identities = 207/458 (45%), Positives = 280/458 (61%), Gaps = 31/458 (6%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVY-----QAGTAVFDHLPLIFAIGIA 59 LQK+GKS MLP++VLP GI+L +G + +P V +AG +VF ++PLIFAIG+A Sbjct: 9 LQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAIGVA 68 Query: 60 IGISKDSNGAAGLSGAISY--------------LMLDAATKTIDKTNNMAVFGGIIAGLI 105 +G + +++G + L+ ++Y L L A + V GGII+G I Sbjct: 69 LGFT-NNDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIAAKHLADTGVLGGIISGAI 127 Query: 106 AGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWML 165 A Y +NRF KLPEYLGFF+G+R VPI++ + I I +WPPI + I +F +W Sbjct: 128 AAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPPIGTAIQTFSQWAA 187 Query: 166 GLGGIGA-GIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTG-----DLARFFAKDPTA 219 + A GI+G R L+P GLHH+ N F Q GEY G D+ R+ A DPTA Sbjct: 188 YQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDPTA 247 Query: 220 GTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMF 279 G ++G F M+GLPAA +A+ +AKP R G+MI ALT+F+TGITEPIEF+FMF Sbjct: 248 GK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFMF 306 Query: 280 LSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAA 339 ++P+LY +HA+L GL+ I LG+R G SFS G ID+++ G + K L +VGICYA Sbjct: 307 VAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGICYAI 366 Query: 340 VYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCAT 399 VY++VF VLIKAL+LKTPGRED D + ++ GGKEN+ +D C T Sbjct: 367 VYYVVFRVLIKALDLKTPGREDATEDSKAGATSEM---APALIAAFGGKENITNLDACIT 423 Query: 400 RLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIG 437 RLR++V D A VD+A LKK GA GVV + G VQ I G Sbjct: 424 RLRVSVADVAKVDQAGLKKLGAAGVVVA-GSGVQAIFG 460 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: 594 Number of extensions: 35 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: 477 Length adjustment: 33 Effective length of query: 419 Effective length of database: 444 Effective search space: 186036 Effective search space used: 186036 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