Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate WP_050655247.1 C1M55_RS19650 phosphoenolpyruvate--protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >NCBI__GCF_002893965.1:WP_050655247.1 Length = 557 Score = 336 bits (862), Expect = 2e-96 Identities = 222/552 (40%), Positives = 300/552 (54%), Gaps = 25/552 (4%) Query: 277 AAVAGTLAGVCASPGLASGPLARLGAI--SLPADDGRHRPEEQHLALDQALQRVRDDVQG 334 A+V +AG+ S G P R + AD PE + + + +AL V +++ Sbjct: 3 ASVDNRIAGIGVSAGSVCAPWLRFSTPEPTSAADPITGSPEAELIRIREALDAVAEELLS 62 Query: 335 SLQQARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQA 394 + + A I + A+ D G++ AA ++ G+ AHA A A CE L A Sbjct: 63 RAKTV----EGVSAEILTTSAAMARDAGIVKAAKANLESGLPTAHAVAVAFDAFCEKLTA 118 Query: 395 LGNLLLAERANDLRDLEKRVLRVLLGDTAPLRVPAGA---IVAAREITPSDLAPLVDAGA 451 LG + AERA DLRDL +R + VL G+ P +PA I+ AR++ P+D A L + Sbjct: 119 LGGYM-AERATDLRDLGQRAVAVLRGEPMP-GIPAPGYPYILVARDLAPADTATLGTSDV 176 Query: 452 AGLCMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRL 511 GL AEGG TSH AILA+S G+P +V +G L EG+ ++LD G + + P A Sbjct: 177 VGLLTAEGGPTSHTAILAKSLGIPAVVNC-SGTDLLAEGKLLILDGTTGTVTIDPSAEMR 235 Query: 512 EQVALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLR 571 E+ L+ + EQ A AQ TRDG + + AN+ + +AA A A +GVGL R Sbjct: 236 ERAVLEASFVAEQ----SASAQGPGRTRDGFAVRLSANIGTLEDAARAGAADCEGVGLFR 291 Query: 572 TEFLFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALG 631 TEF +L R AP EEQ Y VL +KV++RT+D G DK L +L L VEENPALG Sbjct: 292 TEFSYLGRHDAPSVEEQAQTYASVLGHFAGQKVVVRTLDSGSDKPLPFLDLGVEENPALG 351 Query: 632 LRGIHLGQARPELLDQQLRALLRVEPLERCR--ILLPMVSEVDELRAIRRRLGELATQLG 689 +RG+ +G P+ L QL AL ++ PMV+ DE + ELA G Sbjct: 352 IRGLRVGTVYPDTLISQLDALAAAGNATGADLWVMAPMVATADEAKDF----AELARSRG 407 Query: 690 IERLPELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHP 749 I ++ G MIEVP+AAL A + EH DF+SIGTNDLSQY A+DR GLA +D P Sbjct: 408 IGKV---GAMIEVPAAALRAKDILEHLDFVSIGTNDLSQYTCAVDRMAGGLAQLLDPWQP 464 Query: 750 ALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQ 809 A+L LIA A G+ VGVCG ASDPL PVLVGLGV LS+ +G ++ ++ Sbjct: 465 AVLDLIAMVGQAGADAGKPVGVCGESASDPLLAPVLVGLGVTSLSMSVPALGAVRAQLAS 524 Query: 810 LDAAECRRHAQA 821 LD A C+ A A Sbjct: 525 LDLAVCKDMAAA 536 Lambda K H 0.319 0.136 0.390 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: 1067 Number of extensions: 51 Number of successful extensions: 6 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: 842 Length of database: 557 Length adjustment: 39 Effective length of query: 803 Effective length of database: 518 Effective search space: 415954 Effective search space used: 415954 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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