Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate WP_003465872.1 J416_RS04205 PTS transporter subunit EIIC
Query= SwissProt::O34521 (452 letters) >NCBI__GCF_000359605.1:WP_003465872.1 Length = 674 Score = 353 bits (907), Expect = e-102 Identities = 203/484 (41%), Positives = 292/484 (60%), Gaps = 54/484 (11%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGR-----EDVFNIPF------------VYQAGTAVF 47 LQK+GK+ MLP+A+LPA GI++A G + V P+ + +AG VF Sbjct: 8 LQKVGKALMLPVALLPAAGILMAFGTSFAQDQWVEKFPWFGNESVQAVLGVMEEAGGVVF 67 Query: 48 DHLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATKTI-----DKTNNMA------- 95 D+LPL+FA+G+AIG++K +G AGL+ I Y++++ I D T+ A Sbjct: 68 DNLPLLFAVGVAIGLAK-GDGVAGLAAIIGYMIMNVTMGEIGGITDDMTSEAAYESMLGV 126 Query: 96 ------VFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVV 149 VFGGII G++A Y YNRF + +LP++LGFF+G+R VPI+TA ++IL I V Sbjct: 127 PTLGTGVFGGIIVGILAAYMYNRFYNIELPQFLGFFAGKRFVPIITAFSSLILGLIMYAV 186 Query: 150 WPPIQSCINSFGEWMLGLGG-IGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTGD 208 WP Q +N+ +ML + +FG+ R LIP GLHH+ + FWF+FG Y G+ Sbjct: 187 WPFAQDGLNAVSHFMLETNRTLSTFVFGIIERALIPFGLHHIFYSPFWFEFGTYTNAAGE 246 Query: 209 LAR-----FFAK-----DPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMI 258 L R FF + D TAG +MTG FP MMFGLPAA LA+ TAKP ++K G+M Sbjct: 247 LIRGDQTIFFEQLKDGVDFTAGNFMTGKFPFMMFGLPAAALAIYHTAKPERKKVVGGIMF 306 Query: 259 GFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYV 318 ALT+F+TGITEP+EF+F+F++PLL+A+H V GLS + L ++ G +FS G IDY+ Sbjct: 307 SAALTSFLTGITEPLEFSFLFVAPLLFAIHCVFAGLSFMTMYLLDVKIGMTFSGGFIDYL 366 Query: 319 LSYGIAEKPL---LLLLVGICYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQD 375 L +GI +++VG+ ++ +Y+ F I+ NL TPGRE D+ + DE D Sbjct: 367 L-FGIMPNRTDWWWVIIVGLVFSVIYYFGFRFAIQKFNLATPGRE-DEANNAEDEGETDD 424 Query: 376 VNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVI 435 I L +GG+EN+ +D C TRLR++V D VD+ LK+ GA GV++ G ++Q I Sbjct: 425 RPYEI-LTAMGGEENITNLDACITRLRVSVDDKGKVDKDKLKQLGASGVMEV-GNNIQAI 482 Query: 436 IGPN 439 GP+ Sbjct: 483 YGPS 486 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: 800 Number of extensions: 47 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: 674 Length adjustment: 36 Effective length of query: 416 Effective length of database: 638 Effective search space: 265408 Effective search space used: 265408 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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