Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_011386738.1 AMB_RS22220 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >NCBI__GCF_000009985.1:WP_011386738.1 Length = 596 Score = 325 bits (832), Expect = 6e-93 Identities = 209/560 (37%), Positives = 302/560 (53%), Gaps = 15/560 (2%) Query: 278 QAVARPAGETLAPNTLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSA--AESRLLDKA 335 +AV R A G+ + G+A+G L D I PE + AE ++A Sbjct: 8 KAVGRSKATARAELVRDGLGVSRGIAIGTLYLHDAGTITVPELRIPAARLDAECARFNEA 67 Query: 336 IATVDADLDTTVRDASQR--GAVGE--AGIFSVHRVLLEDPTLLDAARDLISLGK-SAGF 390 A ++ ++D + R GA GE + +R +L LL I + +A Sbjct: 68 SANAGRQVEQ-LQDKAGRLGGAAGEELGYLLDAYRQMLHGSRLLRGVEARIRNDRINAEA 126 Query: 391 AWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRALGYTSATART-LPEEAVLAAEE 449 A ++ I + +ED LA R AD++DI +R+LRAL T+ T LP AV+ AEE Sbjct: 127 AVQQEINEIVRGFEAMEDPYLAARVADIKDIGRRLLRALTNTAYRPFTALPRNAVIVAEE 186 Query: 450 FTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNA 509 TP+D + LD ++V L GG+ H AI+AR G+P+++ + D L + G QV+++ Sbjct: 187 MTPADTALLDPNQVAGLATVMGGSEGHTAIMARSLGLPSVLGIADLLTGVKGGEQVIIDG 246 Query: 510 TTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAK 569 T G + P + R ER R R AVT DG I + AN+ ++ Sbjct: 247 TNGLVVINPGPETLAFYRRERAAFLKARRVLSRLKDVPAVTRDGGRITLQANMELPNEVG 306 Query: 570 TAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEV 629 +++GA+ +GLLR+E L+++R P+ DE + +V+ + GRT +RT D G DK Sbjct: 307 AVLDSGAEGIGLLRSEFLYMNRDDVPSEDEQYAILKDVVERMGGRTVTVRTFDAGGDKLA 366 Query: 630 DYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGELIRI 689 L PNP+LGLR IRL R DLL+ QL +L G VRIL+PM+ VGEL Sbjct: 367 PALGCTIGPNPSLGLRAIRLGLARQDLLEAQLAAILRASAHGPVRILIPMIATVGELRAT 426 Query: 690 RKRIDEFARELGRT-----EPI-EVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTL 743 R+ ++ R L + +P+ +G MIE+P AAL AD +A HADF +IGTNDL QYTL Sbjct: 427 REVMNRVIRRLRKAGVSLPDPLPRLGAMIEIPGAALSADSIAWHADFFAIGTNDLVQYTL 486 Query: 744 AMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVT 803 A+DR +A + LHPAVLRLI T Q A + V VCG +AGDP PLL+GLG+ Sbjct: 487 AIDRSDEAVAHLYNPLHPAVLRLIQFTTQAAQRANIPVSVCGEMAGDPRYAPLLLGLGLR 546 Query: 804 ELSVDPVSVPGIKARVRNLD 823 +LS+ ++P +K R+R+LD Sbjct: 547 DLSMSTSNLPVVKNRIRSLD 566 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: 1067 Number of extensions: 40 Number of successful extensions: 2 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: 596 Length adjustment: 39 Effective length of query: 815 Effective length of database: 557 Effective search space: 453955 Effective search space used: 453955 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