Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 268 bits (686), Expect = 3e-76 Identities = 173/485 (35%), Positives = 258/485 (53%), Gaps = 45/485 (9%) Query: 6 FFQRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQ--------AGGAIFDNLALIFA 57 F QRL +AL LPIA+LP A +++ +PFI+ G +F + ++FA Sbjct: 26 FAQRLSQALLLPIAILPAAGVMIGLATNP---IPFISADLATLMWTVGNLVFSMMPMLFA 82 Query: 58 IGVASSWSKDNAGSAALAGAVGYFVMTKA-------------MVTINPEINMGVLAGIIT 104 + +A + +D G AA + GY V + M+ I+ G+ G++ Sbjct: 83 VTIAIGFCRDQ-GIAAFSAVFGYGVFFSSLSALAKIYHLPTEMILGQATIDTGIAGGMMV 141 Query: 105 GLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGE 164 G V I+LP SFF G+R P+ ++LA +F +WP + + I Sbjct: 142 GAFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISN 201 Query: 165 WIV-SAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGD 223 W V A ++G + RLLIP GLH + N + ++G++ N V G++ R+ AGD Sbjct: 202 WAVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEWV-RGEVARYLAGD 260 Query: 224 GTAGMFMSGFFPIMMFGLPGAALAMYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFL 283 AG G+ I M+GLP AALA++ A K R V G++LS A +LTGVTEP+EF Sbjct: 261 PQAGNLAGGYL-IKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFA 319 Query: 284 FLFLAPLLYLLHAVLTGISLFIATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVM 343 F+F+APLL++LHA++TGI+ + +L IH FS G +D+ L L S+NV L++ Sbjct: 320 FMFVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSL---LLGQSRNVEWFLIL 376 Query: 344 GVVFFFVYFLLFSAVIRMFNLKTPGREDKAADVVTEEANSNTEEGLTQLATSYIAAVGGT 403 G + +Y+L+F I FNLKTPGR EA S GL S I A+GG Sbjct: 377 GPLTAVIYYLVFRGAILAFNLKTPGR---------MEAGSGQRAGL----ISMITALGGQ 423 Query: 404 DNLKAIDACITRLRLTVGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMK 463 DN+ + AC+TRLR++V + V+ A +LGA GVV L +Q++ G KAESI ++ Sbjct: 424 DNINELTACLTRLRISVKHAELVDKAQLNKLGAKGVV-LVGNGVQLVYGTKAESIRRLLQ 482 Query: 464 KVVTR 468 + + R Sbjct: 483 RYLDR 487 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: 625 Number of extensions: 24 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: 490 Length adjustment: 36 Effective length of query: 615 Effective length of database: 454 Effective search space: 279210 Effective search space used: 279210 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 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