Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC
Query= SwissProt::O34521 (452 letters) >NCBI__GCF_000313915.1:WP_083848942.1 Length = 553 Score = 187 bits (474), Expect = 1e-51 Identities = 152/543 (27%), Positives = 245/543 (45%), Gaps = 104/543 (19%) Query: 4 FLQKLGKSFMLPIAVLPAVGIILALGR-------EDVFNIPFVYQ-AGTAVFDHLPLIFA 55 F QK GK+ M+ IAV+PA G+++++G+ I V + G A+ +LP++FA Sbjct: 9 FWQKFGKALMVVIAVMPAAGLMISIGKLIAMAQVSLAVTIGGVTENIGWAIIGNLPILFA 68 Query: 56 IGIAIGISKDSNGAAGLSGAISYLMLDAATKTIDKTN----------------------- 92 + I +K+ G A SG +++++++ T + Sbjct: 69 LAIGGSWAKERAGGAFASG-LAFILINRITGAVFGVTKEMLANPEATVHTIFGQKILVNG 127 Query: 93 -----------NMAVFGGIIAGLIAGYTYNRFKD-TKLPEYLGFFSGRRLVPILTAIITI 140 NM VF GIIAG YN++ + KLP L FF+G+R VP + + ++ Sbjct: 128 YFTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGKRFVPFVVILWSV 187 Query: 141 ILAGIFGVVWPPIQSCINSFGEWMLGLGGI----GAGIFGLFNRLLIPLGLHHVLNNIFW 196 I+A + V WP Q+ IN FG+W+ G I+G RLL+P GLHH+L Sbjct: 188 IIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLPFGLHHMLTIPMN 247 Query: 197 FQ--FGEYNGVTGDLA--RFFAKDPTAGTYMTGFFPIMMFG------------------- 233 + G Y+ +TG A +DP ++T + G Sbjct: 248 YTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQLLESIRPARFKV 307 Query: 234 ---------LPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLL 284 L AM +P ++K + + AL F+TG+TEP+EF FMF L Sbjct: 308 GQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEPLEFMFMFAGIPL 367 Query: 285 YAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYV------LSYGIAEKPLLLLLVGICYA 338 Y V+A+L G++ + + + +R + G I+ + + G+ + ++ I + Sbjct: 368 YVVYALLQGVAFGLADIIDLR---LHAFGNIELLTRLPMSIKAGLGMDIINFIITCIVFF 424 Query: 339 AVYFIVFYVLIKALNLKTPGR-----EDDDVDEVLDENTV------QDVNENIM--LKGL 385 + + V +IK ++ TPGR E +D D T + N +M ++ L Sbjct: 425 FLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTATSSTKPSEANNQVMNIIQLL 484 Query: 386 GGKENLQTIDHCATRLRLTVKDTALV-DEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAA 444 GGKEN+ +D C TRLR+TVKDT V DE KK GA G++ VQ + GP + Sbjct: 485 GGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGLIHK-NNGVQAVYGPKADVLK 543 Query: 445 EEL 447 ++ Sbjct: 544 SDI 546 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: 618 Number of extensions: 39 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 452 Length of database: 553 Length adjustment: 34 Effective length of query: 418 Effective length of database: 519 Effective search space: 216942 Effective search space used: 216942 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 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