Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC
Query= SwissProt::O34521 (452 letters) >NCBI__GCF_001277175.1:WP_038857764.1 Length = 499 Score = 317 bits (812), Expect = 6e-91 Identities = 193/490 (39%), Positives = 277/490 (56%), Gaps = 51/490 (10%) Query: 2 LSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIG 61 LS L +G++ MLPI++LPA G++LA G D F++P + AG +FD+LPL+FAIG A+G Sbjct: 11 LSKLSMIGRALMLPISLLPAAGLLLAFG--DKFHLPLMMNAGGVIFDNLPLLFAIGSAVG 68 Query: 62 ISKDSNGAAGLSGAISYLMLDAATKTI-------------------DKTNNMAVFGGIIA 102 ++ +S G A LS A+S +++ T T M VFGG+I+ Sbjct: 69 LASES-GIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQMGVFGGLIS 127 Query: 103 GLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGE 162 G++A + YNRF +LPE+LGFFSG+R V I A ++ +L VW IQ+ I++ Sbjct: 128 GILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAGIDALSV 187 Query: 163 WMLGLGGIGAG-IFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTGDL------------ 209 + G + IFGL R LIPLGLHH+ FW+ FG+Y TG + Sbjct: 188 IVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGDQTIWFKML 247 Query: 210 ---ARFFAKDP--TAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTA 264 + F+ + AG +M G FP+M+F LPAACLAM A +K +G++ ALT Sbjct: 248 EEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGILFSAALTC 307 Query: 265 FITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIA 324 F+TGITEP+EF F+F++P+LY +A++ GL+ + L SFSAG IDY+ S+GI Sbjct: 308 FLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDYI-SFGIL 366 Query: 325 EK-------PLLLLLVGICYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVN 377 L ++VGI A +Y+ F +I+ ++KTPGR DV D+ T ++ Sbjct: 367 PSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRV--DVTASADDKTDAELA 424 Query: 378 ENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIG 437 NI + LGGKEN+ ++ C TRLRL V LVD+ L GA+GVV G +QVI G Sbjct: 425 GNI-VGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQVIFG 483 Query: 438 PNVEFAAEEL 447 +F A+ L Sbjct: 484 ARAQFIAQSL 493 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: 620 Number of extensions: 28 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: 499 Length adjustment: 33 Effective length of query: 419 Effective length of database: 466 Effective search space: 195254 Effective search space used: 195254 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 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