Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 5208528 Shew_1039 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >FitnessBrowser__PV4:5208528 Length = 743 Score = 286 bits (732), Expect = 3e-81 Identities = 197/618 (31%), Positives = 315/618 (50%), Gaps = 19/618 (3%) Query: 220 MMGLAITEQAQVHVSCRGSDAEAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLH 279 ++G+ + +QA + S+AE A L V E A P ++ V Sbjct: 119 ILGVLVVQQADAR---QFSEAEEAFLMTLAAQLAVAVREQRKKAEVKSAP----DKCVYT 171 Query: 280 GVCAAPGLVTGPLVRLSGIQLPEDIGGHA---IEEQRQRLSDALAQVRGEIHLTLEHARA 336 G AA G+V + L G ++P + G ++E+ LS AL R + + Sbjct: 172 GTSAASGVVIAHAMVLGG-EIPLEQQGRRTKQVDEELLALSQALDACRNTLSALSQRFDG 230 Query: 337 RQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLA 396 ++ ++IFSA LL+D L I+ G A A SR QQ+ + Sbjct: 231 ENEKEVQSIFSALQLLLDDTSLGGEYGREIQAGWTAISAVSRVSLRYIDHFQQMQDPYMQ 290 Query: 397 ERANDLRDLRQRVLRVLLG-EAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGG 455 ERA D+RDL QRVLR L+ + Q ++ I+ +E T + L + + G+ GG Sbjct: 291 ERATDIRDLGQRVLRELIEPQKMQLELDVPVILVTKEATATMLAEFPQHKLVGIVTELGG 350 Query: 456 ATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTR 515 SH AILAR G+P ++ + L A G+ ++L+A+ G++ ++PT + + R + Sbjct: 351 VNSHAAILARAFGVPAVIGVEGILNAGIDGKQLILNANRGQVLISPTPTLIGEYRSLISA 410 Query: 516 RTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRH 575 AL+ + PA T+D + + N + +A GADGVGL RTE F+ + Sbjct: 411 EKALQKRYAEELSKPAMTLDERRIHLYLNAGLLSSLASEIAEGADGVGLYRTEIPFMLQT 470 Query: 576 TAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQV 635 P E EQ + Y+ VL A +PV++RT+DVGGDK L YLP+ E NP LG RGIRL Sbjct: 471 RFPSEAEQVEVYRQVLNAALGRPVVMRTLDVGGDKPLSYLPI-IEENPFLGWRGIRLTLD 529 Query: 636 RPDLLDQQLRALLQ-TRPLDRCRILLPMVTEVDELLHIRKRLDALGSELGLS-----ERP 689 P+L QLRA+L + ++ ILLPMV +DE+ L+ E+ +RP Sbjct: 530 HPELFLVQLRAMLNASGGGEQLHILLPMVCCLDEIDQAIAYLEQAYLEVKQDVHPDLQRP 589 Query: 690 QLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRL 749 ++G+M+EVPA E++A+ DF+S+G+NDL+QY LA+DR++ ++ D+ HP +LR Sbjct: 590 KIGIMLEVPALLFQLEEVAKRVDFISVGSNDLTQYLLAVDRNNPRVSTLYDSYHPGILRA 649 Query: 750 IAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQ 809 + Q ++ + VCG LA +P+ +L+ +G +LS++ + +I +R + Sbjct: 650 LTQARLACREYRLPISVCGELAGEPMGVLLLVAMGYTQLSMNQGSLAKINYLIRRVSYQD 709 Query: 810 CARLSNELLNLGSALAVR 827 + L + L+L + VR Sbjct: 710 LSELLAQALSLTNGFEVR 727 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: 1055 Number of extensions: 46 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: 743 Length adjustment: 41 Effective length of query: 796 Effective length of database: 702 Effective search space: 558792 Effective search space used: 558792 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: 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