Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_17535 (571 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 281 bits (719), Expect = 4e-80 Identities = 182/462 (39%), Positives = 257/462 (55%), Gaps = 31/462 (6%) Query: 10 QRLGRALMLPIAILPIAGLLLRLGDTDL----LDIA-IIHDAGQAIFANLAMIFAIGIAV 64 QRL +AL+LPIAILP AG+++ L + D+A ++ G +F+ + M+FA+ IA+ Sbjct: 28 QRLSQALLLPIAILPAAGVMIGLATNPIPFISADLATLMWTVGNLVFSMMPMLFAVTIAI 87 Query: 65 GFARDNNGTAGLAGAIGYLVMIATLKVL-------------DASINMGMLAGIISGLLAG 111 GF RD G A + GY V ++L L A+I+ G+ G++ G Sbjct: 88 GFCRDQ-GIAAFSAVFGYGVFFSSLSALAKIYHLPTEMILGQATIDTGIAGGMMVGAFTC 146 Query: 112 ALYNRFKDIKLPEYLAFFGGRRFVPIVTGFSAVGLGVVFGLIWPPIQQGINGFGALLMES 171 + + I+LP +FF GRR P++ A+ L +F L+WP + I + Sbjct: 147 LVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISNWAVYQ 206 Query: 172 GSFGAF-VFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPATGAVVTGDLSRYFAGDPKGG 230 AF V+G+ RLLI GLHHI N + G + + V G+++RY AGDP+ G Sbjct: 207 EPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEW--VRGEVARYLAGDPQAG 264 Query: 231 QFMTGMFPVMLFGLPAACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFL 290 + G + + ++GLPAA LA++R A R + GI+LS A +LTGVTEPIEFAFMF+ Sbjct: 265 N-LAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAFMFV 323 Query: 291 APLLFLVHALLTGVSMAVTNLLGIHLGFTFSGGFIDMVLGWGKSTNGWLVVPVGLAYAAI 350 APLLF++HAL+TG++ AVT L IH FS G +D L G+S N + +G A I Sbjct: 324 APLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLTAVI 383 Query: 351 YYLVFDFCIRRFDLKTPGREEVPAGDKPAIAENQRAAAYIQALGGADNLITIGACTTRLR 410 YYLVF I F+LKTPGR E +G + + + I ALGG DN+ + AC TRLR Sbjct: 384 YYLVFRGAILAFNLKTPGRMEAGSGQRAGL------ISMITALGGQDNINELTACLTRLR 437 Query: 411 LDMVDRNKASDAQLKALGAMAVVRPGNGGSLQVVVGPMADSI 452 + + AQL LGA VV GNG +Q+V G A+SI Sbjct: 438 ISVKHAELVDKAQLNKLGAKGVVLVGNG--VQLVYGTKAESI 477 Score = 36.2 bits (82), Expect = 3e-06 Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 7/85 (8%) Query: 479 TPAALSSTEAQQ-----WLDALGGQDNVLQLECVATSRLRVRLADDKGLSESRLKGLGCQ 533 TP + + Q+ + ALGGQDN+ +L T RLR+ + + + +++L LG + Sbjct: 399 TPGRMEAGSGQRAGLISMITALGGQDNINELTACLT-RLRISVKHAELVDKAQLNKLGAK 457 Query: 534 GMSSLEDGVWHLLLGEKAPRLWQAL 558 G+ + +GV L+ G KA + + L Sbjct: 458 GVVLVGNGV-QLVYGTKAESIRRLL 481 Lambda K H 0.326 0.142 0.430 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: 661 Number of extensions: 47 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 571 Length of database: 490 Length adjustment: 35 Effective length of query: 536 Effective length of database: 455 Effective search space: 243880 Effective search space used: 243880 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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