Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_004265629.1 C665_RS00525 phosphoenolpyruvate--protein phosphotransferase
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >NCBI__GCF_000310185.1:WP_004265629.1 Length = 576 Score = 317 bits (811), Expect = 2e-90 Identities = 202/569 (35%), Positives = 303/569 (53%), Gaps = 14/569 (2%) Query: 278 LHGVCAAPGLVTGPLVRLSGIQLPED---IGGHAIEEQRQRLSDALAQVRGE-IHLTLEH 333 LHG+ + G+ G + +S L + + ++++ RL +ALA V+GE I L Sbjct: 5 LHGLAVSQGIAIGHVHLVSHALLEVNHYHVAPRYLDDELARLDEALATVQGELIGLKAIT 64 Query: 334 ARARQHRDEEAIFSAHLALLEDPVLLDAA-DLFIEQGSAAPHAWSRSIDTQCQVLQQLGS 392 + H + A L +L DP+L+DAA L E+ A A + ++ + +Q+ Sbjct: 65 TSGQAHSEVGAFVDLQLMMLADPMLVDAARQLVTERRCNAEWALVQQMEHLVEQFRQIED 124 Query: 393 TLLAERANDLRDLRQRVLRVLLGEAWQFDV----AAGAIVAAQELTPSDLLQLSAQGVAG 448 L ER D+ + +R+++VLLG G+IV A +L+P+D + +AG Sbjct: 125 PYLRERQADVVQVVERLVKVLLGHPGHLPPRRRDGLGSIVVAHDLSPADTIGFRDHNIAG 184 Query: 449 VCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQ 508 GG TSH AI+AR +P +V L E + +++D G + + P + + + Sbjct: 185 FVTDVGGPTSHTAIVARSLKIPAVVGLHHVRDLLEDDELIIVDGTRGVIIVAPDEQIVEE 244 Query: 509 VRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTE 568 R ++ R++ L T A T+DG EV + AN+ + + ADG+GL RTE Sbjct: 245 YRLRRSELEIERSKLNRLRDTRAATLDGEEVNLLANIEGPKDLPAVKSANADGIGLYRTE 304 Query: 569 FLFVDRHTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLR 628 FLF+ R T PDEEEQ +AY+AV++A+ KPV IRT DVG DK L+ E NP LGLR Sbjct: 305 FLFIGRDTLPDEEEQYEAYRAVVKALPGKPVTIRTFDVGADKALNGAQAREEPNPALGLR 364 Query: 629 GIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVT---EVDELLHI--RKRLDALGSEL 683 +R + P + QLRALL+ R +I++PM+ EVD+ L + + + + ++ Sbjct: 365 AVRYSLAEPKMFKTQLRALLRASAHGRLQIMVPMLAHAQEVDQCLTLLEKAKAELRAEKI 424 Query: 684 GLSERPQLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALH 743 E ++G M+EVPAAAL FLSIGTNDL QYTLA+DR +A D LH Sbjct: 425 KFDEGIRIGGMIEVPAAALSLGMFIRRLAFLSIGTNDLIQYTLAIDRSDEAVAHLYDPLH 484 Query: 744 PALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVR 803 PA+L+LIA T + A+ G V VCG +A DPL T +L+G+G+R S+ P I EIK +V Sbjct: 485 PAVLKLIAGTISSGARFGLPVSVCGEMAGDPLYTELLLGMGLRNFSMHPGSILEIKQQVL 544 Query: 804 HLDAAQCARLSNELLNLGSALAVRRACHR 832 D + A +L + +R A R Sbjct: 545 RADLGELAPRVQRILKMDEPARIREAVER 573 Lambda K H 0.319 0.134 0.386 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: 970 Number of extensions: 44 Number of successful extensions: 4 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: 837 Length of database: 576 Length adjustment: 39 Effective length of query: 798 Effective length of database: 537 Effective search space: 428526 Effective search space used: 428526 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 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. 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