Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 280 bits (716), Expect = 1e-79 Identities = 173/485 (35%), Positives = 267/485 (55%), Gaps = 50/485 (10%) Query: 6 FFQRLGRALQLPIAVLPVAALLLRFG------QPDLLNVAFIAQAGGAIFDNLALIFAIG 59 F QRL +AL +PIA+LP A ++L P++LNV +A G IF + ++FA+ Sbjct: 27 FAQRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLA-VGKLIFAIMPILFAVA 85 Query: 60 VASSWSKDSAGAAALAGAVGYFVLTKAMVTINP-------------EINMGVLAGIITGL 106 VA + +D G AA GY V+T + + ++ G+ G++ G Sbjct: 86 VAIGFCRDQ-GIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLIGG 144 Query: 107 VGGAAYNRWSD-IKLPDFLSFFGGKR-----FVPIATGFFCLVLAAIFGYVWPPVQHAIH 160 V A RWS I+LP SFF G+R +P+A G L + ++WP + I Sbjct: 145 VTCFAV-RWSQYIRLPAIFSFFEGRRSASLLIIPLAMG-----LGYVLAHIWPSLSLLIE 198 Query: 161 AGGEWIV-SAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRF 219 +W V A+ G++G + RLLIP GLH + N + ++G++ V G++ R+ Sbjct: 199 RVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARY 258 Query: 220 YAGDGTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEP 279 AGD AG G+ I M+GLP AALA++ A R V G++LS A ++LTGVTEP Sbjct: 259 LAGDPQAGNLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEP 317 Query: 280 LEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWM 339 +EF FMF+APLL+L+H +L+G++ FV +L IH FS G +D+ L+++L S+N Sbjct: 318 IEFAFMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSL---SRNTGW 374 Query: 340 LLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAA 399 V+G + IY+++F I FNLKTPGR + + ++E L + IAA Sbjct: 375 FAVLGPLTAVIYYILFRGSILAFNLKTPGR-------LQSDGTKGSKESLRAI----IAA 423 Query: 400 VGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIG 459 +GG DN+ ++AC+TRLRL+V VN +LGA GV+ + K +Q++ G KAE++ Sbjct: 424 LGGRDNIVELNACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGK-GVQIVYGTKAETLR 482 Query: 460 DAMKK 464 +++ Sbjct: 483 KVLQR 487 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: 689 Number of extensions: 36 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: 648 Length of database: 499 Length adjustment: 36 Effective length of query: 612 Effective length of database: 463 Effective search space: 283356 Effective search space used: 283356 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: 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