Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 1153 bits (2983), Expect = 0.0 Identities = 583/648 (89%), Positives = 615/648 (94%), Gaps = 1/648 (0%) Query: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGV 60 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLN++FIAQAGGAIFDNLALIFAIGV Sbjct: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGV 60 Query: 61 ASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKL 120 ASSWSKDSAGAAALAGAVGYFVLTKAMVTINP INMGVLAGIITGLVGGA YNRWS IKL Sbjct: 61 ASSWSKDSAGAAALAGAVGYFVLTKAMVTINPAINMGVLAGIITGLVGGAVYNRWSGIKL 120 Query: 121 PDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFI 180 PDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQ+AIHAGGEWIV AGALGSGIFGFI Sbjct: 121 PDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGSGIFGFI 180 Query: 181 NRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFG 240 NRLLIPTGLHQVLNTIAWFQIGEFTNAAG VFHGDINRFYAGDGTAGMFMSGFFPIMMFG Sbjct: 181 NRLLIPTGLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYAGDGTAGMFMSGFFPIMMFG 240 Query: 241 LPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTG 300 LPGAALAMYFAAPKERRPMVGGMLLSVA+TAFLTGVTEPLEFLFMFLAPLLYLLHA+LTG Sbjct: 241 LPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTG 300 Query: 301 ISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIR 360 ISLFVAT LGIHAGFSFSAGAIDY LMY+LPAAS+NVWML+VMGV+FF IYF++FS VIR Sbjct: 301 ISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIR 360 Query: 361 MFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTV 420 MFNLKTPGREDK D++VTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTV Sbjct: 361 MFNLKTPGREDKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTV 420 Query: 421 ADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATP 480 ADSA VND CKRLGASGVVKLNKQTIQVIVGAKAES+GD MKKVVARGPVAAA+A + Sbjct: 421 ADSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAASHS 480 Query: 481 A-TAAPVAKPQAVPNAVSIAELVSPITGDVVALDQVPDEAFASKAVGDGVAVKPTDKIVV 539 A AA KPQAV NA ++ LVSPITGD+VAL+QVPDEAFASKAVGDGVAVKPTDKIVV Sbjct: 481 APVAAQAVKPQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVV 540 Query: 540 SPAAGTIVKIFNTNHAFCLETEKGAEIVVHMGIDTVALEGKGFKRLVEEGAQVSAGQPIL 599 +PAAGT+VKIFNTNHAFCLETE GAEIVVHMGIDTVAL G+GFKRLVEEGA+V AG+PIL Sbjct: 541 APAAGTVVKIFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPIL 600 Query: 600 EMDLDYLNANARSMISPVVCSNIDDFSGLIIKAQGHIVAGQTPLYEIK 647 E+DL++LNANARSMISPVVCSN DD+S L+I+A G +VAGQTPLYEIK Sbjct: 601 ELDLEFLNANARSMISPVVCSNSDDYSALVIQATGKVVAGQTPLYEIK 648 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: 1357 Number of extensions: 42 Number of successful extensions: 2 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: 650 Length adjustment: 38 Effective length of query: 610 Effective length of database: 612 Effective search space: 373320 Effective search space used: 373320 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: 54 (25.4 bits)
This GapMind analysis is from Sep 17 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