Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_019616713.1 G327_RS0120665 PTS transporter subunit EIIC
Query= BRENDA::P09323 (648 letters) >NCBI__GCF_000381745.1:WP_019616713.1 Length = 485 Score = 394 bits (1012), Expect = e-114 Identities = 217/501 (43%), Positives = 302/501 (60%), Gaps = 53/501 (10%) Query: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQ--------PDLLNVAFIAQAGGAIFDNL 52 MNILG+FQ++GRAL +P+AVLP AA+L+ G + AF+ +AG A+ DN+ Sbjct: 1 MNILGYFQKVGRALMVPVAVLPAAAILMGIGYWIDPNGWGGESQLAAFLIKAGAAVIDNM 60 Query: 53 ALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGV-------------- 98 +++FA+GVA SKD GAAAL+G VG+ V+T ++P G+ Sbjct: 61 SILFAVGVAYGMSKDKDGAAALSGLVGFLVVT---TLLSPGAVAGIQGIPASEVPFAFNK 117 Query: 99 ----LAGIITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPP 154 GI+ G++ YNR+S ++L L+FF G+R VPI ++++ I VWP Sbjct: 118 INNQFVGILVGIISAELYNRFSSVELHKALAFFSGRRLVPIVVSVVMILVSFILMAVWPM 177 Query: 155 VQHAIHAGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHG 214 + + GE I G +G+G++ F NRLLIP GLH LN++ WF + Sbjct: 178 IFGGLQHFGETISGLGEVGAGLYAFFNRLLIPVGLHHALNSVFWFDVAGIN--------- 228 Query: 215 DINRFYAGD----------GTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGML 264 DI F +G G GM+ +GFFPIMMFGLPGAA A+Y AA E + V ++ Sbjct: 229 DIPNFLSGQTGIDAGTAIIGKTGMYQAGFFPIMMFGLPGAAFAIYTAAKPENKEKVASIM 288 Query: 265 LSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDY 324 L+ A+ +F TGVTEPLEF FMF AP+LY++HA+L+G+S+F A + AGF FSAG +D Sbjct: 289 LAAALASFFTGVTEPLEFSFMFAAPVLYVIHAVLSGVSVFFAASMEWMAGFGFSAGLVDL 348 Query: 325 ALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSN 384 L P A++ +ML+V G+ FFAIY+ F VI+ +LKTPGRED E+ + Sbjct: 349 VLSSQNPLATK-WYMLIVQGIAFFAIYYFTFLAVIKGLDLKTPGREDAEE----NAPKTK 403 Query: 385 TEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNK 444 T E +LAT Y+AA+GG +NL+ IDACITRLRLT+ D + N+ K LGA GVVKL + Sbjct: 404 TTEDAGELATQYVAALGGINNLEVIDACITRLRLTLKDRSEANEAELKALGAMGVVKLGE 463 Query: 445 QTIQVIVGAKAESIGDAMKKV 465 +QVI+G +AESI + MK V Sbjct: 464 NNLQVIIGPQAESIANRMKAV 484 Lambda K H 0.324 0.139 0.408 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: 820 Number of extensions: 39 Number of successful extensions: 6 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: 648 Length of database: 485 Length adjustment: 36 Effective length of query: 612 Effective length of database: 449 Effective search space: 274788 Effective search space used: 274788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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