Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__BFirm:BPHYT_RS02745 Length = 591 Score = 479 bits (1233), Expect = e-139 Identities = 236/462 (51%), Positives = 318/462 (68%), Gaps = 15/462 (3%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64 +Q+LG++ MLPIAVLP G++L LG+ DVFNI + AG A+FD+LPL+FAIG+A+G +K Sbjct: 9 IQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAK 68 Query: 65 DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124 D+NG AGL+GAI YL+ A K I+ NM V GI+AG++AG YNR+KD KLP+YL F Sbjct: 69 DNNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAF 128 Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184 F G+R VPI+T ++ ++L FG VW P+Q+ I++ G W+ G +GA +FG+ NRLL+ Sbjct: 129 FGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLV 188 Query: 185 LGLHHVLNNIFWFQFGEYN-----GVTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAACL 239 GLHH+LN++ WF FG + VTGDL RFFA DPTAGT+MTGFFP+MMFGLPAACL Sbjct: 189 TGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACL 248 Query: 240 AMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIV 299 AM A +R G++ ALT+F+TG+TEPIEF+FMFL+P+LY +HA+LTG+SL I Sbjct: 249 AMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAIC 308 Query: 300 NWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGR 359 + LGI GF+FSAGAIDYVL+YG++ + + +G+ Y VY+ +F I+ N+ TPGR Sbjct: 309 SALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATPGR 368 Query: 360 E----DDDVDEVLDENTVQDVNENIM------LKGLGGKENLQTIDHCATRLRLTVKDTA 409 E D+ VD V V + + LGG NL +D C TRLRL+V D+ Sbjct: 369 EPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSN 428 Query: 410 LVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451 V E LK GA+GV+K G +VQVIIGP + A+E+R + Sbjct: 429 KVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVI 470 Score = 28.1 bits (61), Expect = 8e-04 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 4/63 (6%) Query: 386 GGKENLQTIDH-CATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAA 444 GG N+ ++D ATRLR+ V+D + VD L + + +++G + A Sbjct: 517 GGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWI---SADTFHIVVGDAAQRYA 573 Query: 445 EEL 447 E+L Sbjct: 574 EKL 576 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: 784 Number of extensions: 44 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 452 Length of database: 591 Length adjustment: 35 Effective length of query: 417 Effective length of database: 556 Effective search space: 231852 Effective search space used: 231852 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