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::P45604 (651 letters) >FitnessBrowser__Koxy:BWI76_RS08220 Length = 650 Score = 1182 bits (3059), Expect = 0.0 Identities = 601/651 (92%), Positives = 626/651 (96%), Gaps = 1/651 (0%) Query: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGV 60 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLN+ FIAQAGGAIFDNLALIFAIGV Sbjct: 1 MNILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGV 60 Query: 61 ASSWSKDNAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNRWAGIKL 120 ASSWSKD+AG+AALAGAVGYFV+TKAMVTINP INMGVLAGIITGLV GAVYNRW+GIKL Sbjct: 61 ASSWSKDSAGAAALAGAVGYFVLTKAMVTINPAINMGVLAGIITGLVGGAVYNRWSGIKL 120 Query: 121 PDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFI 180 PDFLSFFGGKRFVPIATGFFCL+LAAIFGYVWPPVQ+AIH+GGEWIV AGALGSGIFGFI Sbjct: 121 PDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGSGIFGFI 180 Query: 181 NRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFG 240 NRLLIPTGLHQVLNTIAWFQIGEFTNAAG VFHGDINRFYAGDGTAGMFMSGFFPIMMFG Sbjct: 181 NRLLIPTGLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYAGDGTAGMFMSGFFPIMMFG 240 Query: 241 LPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTG 300 LPGAALAMY AAPK RRPMVGGMLLSVAITAFLTGVTEPLEFLF+FLAPLLYLLHA+LTG Sbjct: 241 LPGAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTG 300 Query: 301 ISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIR 360 ISLF+ATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWML+VMGVVFF +YFLLFSAVIR Sbjct: 301 ISLFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIR 360 Query: 361 MFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDACITRLRLTV 420 MFNLKTPGREDK DVVTEEANSNTEEGLTQLAT+YIAAVGGTDNLKAIDACITRLRLTV Sbjct: 361 MFNLKTPGREDKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTV 420 Query: 421 GDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMKKVVTRGPVAAAAAAPAG 480 DSA VNDAACKRLGASGVVKLNKQTIQVIVGAKAES+GDEMKKVV RGPVAAAAAA + Sbjct: 421 ADSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAA-SH 479 Query: 481 NVATAAPAAKPQAVANAKTVESLVSPITGDVVALEQVPDEAFASKAVGDGIAVKPTDNIV 540 + AA A KPQAVANAKTVE+LVSPITGD+VALEQVPDEAFASKAVGDG+AVKPTD IV Sbjct: 480 SAPVAAQAVKPQAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIV 539 Query: 541 VAPAAGTVVKIFNTNHAFCLETNNGAEIVVHMGIDTVALEGKGFKRLVEEGTDVKAGEPI 600 VAPAAGTVVKIFNTNHAFCLET NGAEIVVHMGIDTVAL G+GFKRLVEEG +VKAGEPI Sbjct: 540 VAPAAGTVVKIFNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPI 599 Query: 601 LEMDLDFLNANARSMISPVVCSNSDDYSALVILASGKVVAGQTPLYEIKGK 651 LE+DL+FLNANARSMISPVVCSNSDDYSALVI A+GKVVAGQTPLYEIKGK Sbjct: 600 LELDLEFLNANARSMISPVVCSNSDDYSALVIQATGKVVAGQTPLYEIKGK 650 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: 1311 Number of extensions: 44 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: 651 Length of database: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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: 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