Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 200507 SO1332 phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI ptt file)
Query= reanno::pseudo5_N2C3_1:AO356_17540 (837 letters) >FitnessBrowser__MR1:200507 Length = 744 Score = 269 bits (688), Expect = 4e-76 Identities = 192/618 (31%), Positives = 309/618 (50%), Gaps = 19/618 (3%) Query: 220 MMGLAITEQAQVHVSCRGSDAEA-ALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVL 278 ++G+ + +QA G +A L A L L ++A S+ ++ + Sbjct: 119 VVGVIVVQQASARQFSEGEEAFLMTLAAQLAMAIRGLKQKAQVSSLH--------QQILF 170 Query: 279 HGVCAAPGLVTGPLVRLSG-IQLPE-DIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARA 336 G A+ G+ L G I L + DI I + RL A+ + + I + Sbjct: 171 QGTSASSGIAIAHAFVLGGEISLEQPDIRCEDIVLESNRLVAAMGRCKEAIGALSQRFDR 230 Query: 337 RQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLA 396 Q + +IF+A LL+D L + G A A SR Q + L Sbjct: 231 EQDEEVASIFNALQLLLDDASLGGEYAREVLLGWEAESAVSRVSLRYIQQFLAMEDPYLK 290 Query: 397 ERANDLRDLRQRVLRVLLG-EAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGG 455 ERA+D+RDL Q+VLR L+ E + + I+ +E + L + Q +AG+ GG Sbjct: 291 ERASDIRDLGQKVLRQLIEPERLELEPDKPVILVTKEADATMLAEFPRQKLAGIVTELGG 350 Query: 456 ATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTR 515 SH AILAR G+P + + L A + +V++A G+L ++P+ +++ R + Sbjct: 351 VNSHAAILARALGVPAITGVEQLLSADIDQKLLVVNASRGQLMVSPSPAIVSEYRSLISA 410 Query: 516 RTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRH 575 + AL+ Q P+ +DG + + N + +A GADG+GL RTE F+ + Sbjct: 411 QKALQRQYAQELTLPSVMLDGKRIRLYLNAGLLSGVASEIAEGADGIGLYRTEIPFMLQQ 470 Query: 576 TAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQV 635 P E EQ + YQ VL A +PV++RT+DVGGDK L Y P+ E NP LG RGIRL+ Sbjct: 471 RFPSESEQVKVYQQVLSAASGRPVVMRTLDVGGDKPLPYFPI-KEDNPFLGWRGIRLSLD 529 Query: 636 RPDLLDQQLRALLQTRPLDR-CRILLPMVTEVDELLHIRKRLDALGSEL-----GLSERP 689 P+L QLRA+LQ + ILLPMV+ +DE+ L+ EL + P Sbjct: 530 HPELFLVQLRAMLQAGAEGKQLSILLPMVSNLDEIDQALAYLEQAHVELKNDVNSNIKMP 589 Query: 690 QLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRL 749 ++G+M+EVPA +++A+ DF+S+G+NDL+QY LA+DR++ +++ D+ HP +LR Sbjct: 590 RIGIMLEVPAMLYQLDEVAKRVDFVSVGSNDLTQYLLAVDRNNPRVSSLFDSYHPGILRA 649 Query: 750 IAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQ 809 + Q H + +CG LA +P+ +L+ +G +LS++ + I +R + Sbjct: 650 LHQARLDCEYHHLDISICGELAGEPMGAILLVAMGYHQLSMNQGSLARINYLLRRVSGED 709 Query: 810 CARLSNELLNLGSALAVR 827 A+L + L+L + VR Sbjct: 710 LAQLLAQALSLSNGFQVR 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: 1022 Number of extensions: 43 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: 744 Length adjustment: 41 Effective length of query: 796 Effective length of database: 703 Effective search space: 559588 Effective search space used: 559588 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