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 GFF3291 Psest_3355 phosphoenolpyruvate-protein phosphotransferase
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__psRCH2:GFF3291 Length = 960 Score = 455 bits (1171), Expect = e-132 Identities = 272/678 (40%), Positives = 383/678 (56%), Gaps = 26/678 (3%) Query: 180 VAHHGGLHARPAALLRKTAQGFSSQAELHFAGQVA---SVDSLVGIMGLGVAEQDEVEVI 236 +A+ GLHARPA +L + AQ F + + AG + SV SL ++ +G +E + Sbjct: 289 LANAHGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQLLEFM 348 Query: 237 CRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLA------------ 284 + AL AL+ A+ + P APGE + P A A Sbjct: 349 AEPAIASDALPALVRAVEEGLGEEVEPLP---APGEASEPPVTAQGPAESAIDQAALRAG 405 Query: 285 ----GVCASPGLASGPLARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQAR 340 G+ ASPG+A GP+ + P + LD AL +V D+ + +++ Sbjct: 406 DQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDESQ 465 Query: 341 LGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLL 400 + + IF+ H A+L+DP L + + + +G+ A AW I++ + +AL + LL Sbjct: 466 VASIRD---IFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLL 522 Query: 401 AERANDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGG 460 AERA DLRD+ +RVL L G A I+ E+ PSD+A L AG+ A GG Sbjct: 523 AERAADLRDVGRRVLACLTGVEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAGGG 582 Query: 461 ATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQ 520 ATSH AI+AR+ G+P +V G G+L L ++LD +G L ++P +LEQ + A Sbjct: 583 ATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERAA 642 Query: 521 REEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERR 580 REE++ A+TRDG +EI AN+ + E EA A GA+G+GLLRTE +F+ Sbjct: 643 REERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNHS 702 Query: 581 AAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQA 640 AP++ Q Y+ VL+A+ R +++RT+DVGGDK L Y P+P EENP LG+RGI L Sbjct: 703 QAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLSLQ 762 Query: 641 RPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMI 700 RP++L+ QLRALL RI+ PMV +DE R + + L +L + L ++G+MI Sbjct: 763 RPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADL-QVGIMI 821 Query: 701 EVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCA 760 E+PSAAL+A LA+ DF SIGTNDL+QY LA+DR H L+ + D LHPA+LRLI T Sbjct: 822 EIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGMTVE 881 Query: 761 GAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQ 820 A HG+WVGVCG LA+D LA P+LVGLGV+ELSV + +K RVR+LD A C+R AQ Sbjct: 882 AAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQRLAQ 941 Query: 821 ALLDLGSARAVRDACLQH 838 L L A VR +H Sbjct: 942 QALMLPGAHEVRAFVGEH 959 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: 2036 Number of extensions: 115 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: 842 Length of database: 960 Length adjustment: 43 Effective length of query: 799 Effective length of database: 917 Effective search space: 732683 Effective search space used: 732683 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: 56 (26.2 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