Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF3781 HP15_3723 PTS system, glucose-specific EIIA/HPr/phosphoenolpyruvate-protein phosphotransferase components
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__Marino:GFF3781 Length = 978 Score = 452 bits (1164), Expect = e-131 Identities = 303/738 (41%), Positives = 408/738 (55%), Gaps = 31/738 (4%) Query: 123 VSVIAIANSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQQV 182 V +A + +++ER+ L AG+ P+ G +AEA S + +V Sbjct: 263 VFCLAGPGDECHDLLERIDTFL--AGDEPI------QGLSAEALLARLSGEAADAVTAKV 314 Query: 183 TLVHAGGLHARPAARAREAARGFDARVEVRY-EGRKAAIE--SVVGLLGLGAGEGATVEL 239 TL++ GLHARPA + + AR +A + +R EG AA+ S+ ++GLGA G T+ L Sbjct: 315 TLLNTHGLHARPAKQLVQEARRHNASIRLRLLEGEGAAVSATSLTRVIGLGARRGQTLLL 374 Query: 240 LGMGPQAAAAVAAIANELTREAHGEVEEK--PARQSSP---APQAVARPAGETLAPNTLA 294 G A+ A+ + LT G + EK P R + P P+A PA P + Sbjct: 375 SATGDDASQAIQS----LTSAIEGGLGEKVSPLRSADPQTKVPEAEQAPALTDDQP--VK 428 Query: 295 GVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRG 354 V A+PG+A+ ++ P+ A + RL ++A+ + D L T +R A Sbjct: 429 AVAASPGLALAPAFVMRQPTLEYPQFAEDSEQQIQRL-NQAVDSADGQLRTLIRQAEGGE 487 Query: 355 AVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAER 414 A A I SVH +L+D L A + I+ G SA W +AI + D LLAER Sbjct: 488 A---APILSVHVEMLQDEDLYQATLEAINEGASAEAGWWKAIDTAARGQEALADRLLAER 544 Query: 415 AADLRDIEKRVLRAL-GYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGA 473 AADLRD+ +RVL L G T P +L A++ PSD++ LD +RV LV ARGGA Sbjct: 545 AADLRDVGRRVLSNLCGVAMPTPPDTPY--ILVADDLGPSDVARLDTTRVRGLVTARGGA 602 Query: 474 TSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRL 533 TSH+AILAR G+PA+V G+ + I G+ +VV+ G L P E+ R +L Sbjct: 603 TSHSAILARALGLPAVVGTGERILTILNGSDLVVDGERGCLVPNPGAERCEKIRRRLQQL 662 Query: 534 ADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAA 593 ++ Q A T DG IEV AN+ AVE GAD VGLLRTE +F+ Sbjct: 663 DALQAEAHENRNQPATTVDGHTIEVCANLGNTAHTPDAVERGADGVGLLRTEFIFMAHPE 722 Query: 594 APTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVR 653 AP YQ DAL+G + RTLDVG DK +DY LP E NP LG+RGIRL+ R Sbjct: 723 APDLATQVTEYQHAFDALNGLPLVARTLDVGGDKPLDYWPLPQEDNPFLGMRGIRLSLTR 782 Query: 654 PDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIE 713 PD+L+ Q+R LL +RI+ PMV D+ E R + + E+ + ++VGVMIE Sbjct: 783 PDILETQVRALLTAAGDRPLRIMFPMVKDLEEFRAARAIVTKVQSEVSASN-VQVGVMIE 841 Query: 714 VPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQG 773 VPS ALLA LA DF SIGTNDLTQYTLA+DR L+A++DGLHP+VLRLI TV+ Sbjct: 842 VPSCALLASTLAPEVDFFSIGTNDLTQYTLAIDRGHGQLSAESDGLHPSVLRLIRMTVEA 901 Query: 774 ADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQD 833 A H +WVGVCG LA DP A+P+LVGL V ELSV VP +KA +R L+ + RQ+A+ Sbjct: 902 AHAHNRWVGVCGELASDPQAIPVLVGLDVDELSVTSRRVPLVKACIRGLNLENARQQAEK 961 Query: 834 ALALESAQAVRAASRETW 851 AL+L +A VR A E W Sbjct: 962 ALSLATASEVRDA-LEAW 978 Lambda K H 0.317 0.133 0.371 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: 1758 Number of extensions: 87 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: 854 Length of database: 978 Length adjustment: 43 Effective length of query: 811 Effective length of database: 935 Effective search space: 758285 Effective search space used: 758285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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