Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= BRENDA::P45604 (651 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 272 bits (695), Expect = 3e-77 Identities = 172/510 (33%), Positives = 266/510 (52%), Gaps = 55/510 (10%) Query: 6 FFQRLGRALQLPIAVLPVAALLLRFGQP----DLLNV-------------PFIAQAGGAI 48 FFQ+LG+ LP+A+L ++L G D++ + ++++ G Sbjct: 14 FFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFA 73 Query: 49 FDNLALIFAIGVASSWSKDNAGSAALAGAVGYFVMTKAM--------------------- 87 F L ++F I + +++N G AA AG +GY VM A+ Sbjct: 74 FSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKAN 133 Query: 88 ----VTINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFFGGKRFVPIATGFFCLI 143 + I+ G+L +I G++ ++ R+ I+LPD L+FFGG RFVPI + + Sbjct: 134 NIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGL 193 Query: 144 LAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQ--- 200 + + VWP I G I SAG G +FG RLL+P GLH +L + F Sbjct: 194 VGLVIPLVWPIFAMGISGLGHMINSAGDFGPMLFGTGERLLLPFGLHHILVALIRFTDAG 253 Query: 201 -----IGEFTNAAGTVFHGDIN--RFYAGDGTAGMFMS-GFFPIMMFGLPGAALAMYLAA 252 G+ + A T+F ++ + +A F+S G P + GLPGAALAMY A Sbjct: 254 GTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHCA 313 Query: 253 PKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIATALGIH 312 R + G+L+S I + G TEPLEFLFLF+AP+LY++HA+LTG+ + + LG+ Sbjct: 314 RPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGVT 373 Query: 313 AGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKTPGREDK 372 G + ID+V+ L S +M+ V+ ++F VY+++F I FNLKTPGR+ + Sbjct: 374 IG-NTDGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRDSE 432 Query: 373 AADVVTEEANSNTEEGLTQLATSYIAAVGGTDNLKAIDACITRLRLTVGDSAKVNDAACK 432 A + E+A + + + A+GG DN+ ++D CITRLRL+V D + VN A K Sbjct: 433 VASSI-EKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQALK 491 Query: 433 RLGASGVVKLNKQTIQVIVGAKAESIGDEM 462 A GVV+LN+ +QV++G + +S+ DEM Sbjct: 492 DNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521 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: 783 Number of extensions: 45 Number of successful extensions: 5 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: 530 Length adjustment: 37 Effective length of query: 614 Effective length of database: 493 Effective search space: 302702 Effective search space used: 302702 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