Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BWI76_RS16295 BWI76_RS16295 bifunctional PTS system maltose and glucose-specific transporter subunits IICB
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Koxy:BWI76_RS16295 Length = 530 Score = 257 bits (656), Expect = 7e-73 Identities = 166/512 (32%), Positives = 262/512 (51%), Gaps = 72/512 (14%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGRE----DVFNI-----------PFVY--QAGTAV 46 F Q+LGK+FMLP+A+L GI+L +G DV + F++ + G+ Sbjct: 14 FFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVLTLLPWLDVPLLQAVFIWMGKVGSFA 73 Query: 47 FDHLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATK--------------TIDKTN 92 F LP++F I I +G+++++ G A +G + Y +++ A + K N Sbjct: 74 FSFLPVMFCIAIPLGLARENKGVAAFAGFVGYAVMNLAVNFWLTAKGILPTTDAAVLKAN 133 Query: 93 NM-----------AVFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITII 141 N+ + G +IAG+I + RF + +LP+ L FF G R VPI+T ++ + Sbjct: 134 NIQNIIGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIITTVVLGL 193 Query: 142 LAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGE 201 + + ++WP IN+ G+ + G G IFG RLL+P GLHH+L + +F E Sbjct: 194 VGLVIPLIWPVFAMGINALGQVINSAGDFGPMIFGTGERLLLPFGLHHIL--VALIRFTE 251 Query: 202 YNG--------VTGDLARFFAKDPTAGTY----------MTGFFPIMMFGLPAACLAMVV 243 G V+G L F A+ T+ G P + GLP A LAM Sbjct: 252 AGGTMDVCGHSVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYH 311 Query: 244 TAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLG 303 A+P R G++I + + G TEP+EF F+F++P+LY +HA+LTGL ++ LG Sbjct: 312 CARPENRHKIKGLLISGVIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTMMAILG 371 Query: 304 IRSGFSFSAGAIDYV---LSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGRE 360 + G + ID+V + +G++ K L+ +V + AVY+ +F I NLKTPGR Sbjct: 372 VTIG-NTDGNVIDFVVFGILHGLSTKWYLVPVVAAIWFAVYYGIFRFAITRFNLKTPGR- 429 Query: 361 DDDVDEVLDENTV-----QDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEAL 415 D + + ++ N +L LGG EN+ ++D+C TRLRL+V D + VD A Sbjct: 430 DIETNSAFEKAVTGVTGKSGYNVPAILAALGGAENIVSLDNCITRLRLSVNDMSKVDSAA 489 Query: 416 LKKAGAKGVVKSGGQSVQVIIGPNVEFAAEEL 447 LK A GVV+ ++QV+IGP V+ +E+ Sbjct: 490 LKANRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 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: 668 Number of extensions: 53 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: 452 Length of database: 530 Length adjustment: 34 Effective length of query: 418 Effective length of database: 496 Effective search space: 207328 Effective search space used: 207328 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: 52 (24.6 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