Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate HSERO_RS00450 HSERO_RS00450 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__HerbieS:HSERO_RS00450 Length = 595 Score = 283 bits (725), Expect = 2e-80 Identities = 197/578 (34%), Positives = 290/578 (50%), Gaps = 24/578 (4%) Query: 288 LAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRL--LDKAIATVDADLDT 345 +A +L G+ + G+A+G+ A +D E+ + L A+ V +L T Sbjct: 1 MASFSLHGIAVSQGIAIGRAHLMAPAALDVKHYLIAADQVEAEIERLKSAVKAVHQELHT 60 Query: 346 TVRDASQRGAVGEAGIF-SVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQIAIL 403 +R R A E G F VH ++L DP L + +D+I +A +A I A Sbjct: 61 -IRSELPREAPPELGAFIDVHSLILSDPMLAEVPQDIIRHRYYNAEWALVTQIEELSAQF 119 Query: 404 TNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEA------VLAAEEFTPSDLST 457 IED L ER AD++ + +R+L+ L + +A LP ++ A + +P+D+ Sbjct: 120 DEIEDPYLRERKADIQQVGERILKVL---TGSATHLPPSGEAAANIIIVAHDISPADMLQ 176 Query: 458 LDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFA 517 S V GG SH AI+AR IPA V + +A + ++++ G + Sbjct: 177 FRESTFAGFVTDLGGPNSHTAIVARSLAIPAAVGMHNASVLVKHDDVLIIDGDAGVVIVD 236 Query: 518 PTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGAD 577 P+ L + + R + RL R+ R + A+T DG I + ANI DA TA E GA Sbjct: 237 PSPLVLAQYRARQERLLRERKKLSRLKKTPAITQDGEPITLLANIELPGDAVTAFEAGAM 296 Query: 578 SVGLLRTELLFIHRAAA----PTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLT 633 +GL R+E LF+ RA P+ DE + Y+ V A+ GR+ IRTLDVGADK +D Sbjct: 297 GIGLFRSEFLFMGRAGHLEKFPSEDEQFEHYKQAVIAMKGRSVTIRTLDVGADKPLDE-D 355 Query: 634 LPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRIRKRI 693 NPALGLR IR P + QLR +L G +++L+PM+ E+ + I Sbjct: 356 EETALNPALGLRAIRYCLSEPQMFLTQLRAILRASAFGPIKLLVPMMAHAFEIDQTLAMI 415 Query: 694 DEFARELGRT-----EPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRC 748 D+ ++L E I VG MIE+P+AAL + DFLSIGTNDL QYTLA+DR Sbjct: 416 DQAKQQLRERKQKFDEEIPVGAMIEIPAAALALPLFVKRLDFLSIGTNDLIQYTLAIDRV 475 Query: 749 QADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVD 808 ++A D LHPAVL L++ + K G V VCG +AGD LL+G+G+ E S+ Sbjct: 476 DHEVAHLYDPLHPAVLFLLSTVISQGRKAGIPVSVCGEMAGDLKWTRLLLGMGLLEFSMH 535 Query: 809 PVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846 P + +K + N D +L + + L A+ AA Sbjct: 536 PSQILSVKNEILNSDLRLLEPQVKKVLRATEPAAITAA 573 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: 1016 Number of extensions: 47 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: 595 Length adjustment: 39 Effective length of query: 815 Effective length of database: 556 Effective search space: 453140 Effective search space used: 453140 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: 55 (25.8 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