Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_019614095.1 G327_RS0107245 PTS glucose transporter subunit IIBC
Query= BRENDA::P45604 (651 letters) >NCBI__GCF_000381745.1:WP_019614095.1 Length = 483 Score = 356 bits (913), Expect = e-102 Identities = 197/476 (41%), Positives = 297/476 (62%), Gaps = 26/476 (5%) Query: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQ------PDLLNVPFIAQAGGAIFDNLAL 54 MNI G Q++G++L LP++VLP+A +LL G PD+++ + QAGGA+F N+AL Sbjct: 1 MNIFGSLQKVGKSLMLPVSVLPIAGILLGVGAAKFSVLPDVVS-QLMEQAGGAVFGNMAL 59 Query: 55 IFAIGVASSWSKDNAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNR 114 +FAIGVA ++K N G A LA AVGY++M + + T+ P N GVL GII G +A A++NR Sbjct: 60 LFAIGVALGFTK-NDGVAGLAAAVGYYIMMQTVETLAPGANTGVLGGIIAGGIAAAMFNR 118 Query: 115 WAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAG-ALG 173 + I LPD+L FF GKR VPI TG +I+ A+ +WPP+ AI S +W + Sbjct: 119 FYNITLPDYLGFFAGKRAVPIMTGLSAIIMGAVLAVIWPPIGSAIASFSDWAAHQNPTVA 178 Query: 174 SGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGF 233 GI+G + R LIP GLH + N +F+ G T+A G +G + + + D T +GF Sbjct: 179 FGIYGVVERSLIPFGLHHIWNVPFFFEAGSCTSATGEQLNGILTCYLSADDTTRAAGNGF 238 Query: 234 ------FPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFL 287 + MFGLP AA+A+ AA R V G++ S A+T+FLTG+TEP+EF FLF+ Sbjct: 239 GQLAGGYMFKMFGLPAAAIAIAHAAKPENRAKVMGIMASAALTSFLTGITEPIEFAFLFV 298 Query: 288 APLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVF 347 AP+LY +HA+L G + + LG+ G SFS G ID+++ L A ++ + +V+G+++ Sbjct: 299 APVLYAVHALLAGSAFVVTNMLGMVHGTSFSHGLIDFLV---LSANAEKMIYFVVIGLIY 355 Query: 348 FFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLK 407 VY+ +F VI+ +LKTPGRE+ EEA + G +++ +AA GG N++ Sbjct: 356 AAVYYTVFRVVIKALDLKTPGREE-------EEAEEAVQLGSSEIPVLLVAAFGGKANIE 408 Query: 408 AIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMK 463 +DACITRLR++V + A V+ A K+LGA+GVV ++ +Q I G K++++ +M+ Sbjct: 409 NLDACITRLRISVHNIALVDKAELKKLGAAGVV-ISGNGVQAIFGTKSDNLKTDME 463 Lambda K H 0.323 0.138 0.406 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: 734 Number of extensions: 42 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: 651 Length of database: 483 Length adjustment: 36 Effective length of query: 615 Effective length of database: 447 Effective search space: 274905 Effective search space used: 274905 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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