Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate BWI76_RS27885 BWI76_RS27885 PTS alpha-glucoside transporter subunit IICB
Query= reanno::pseudo5_N2C3_1:AO356_17535 (571 letters) >FitnessBrowser__Koxy:BWI76_RS27885 Length = 540 Score = 238 bits (607), Expect = 5e-67 Identities = 181/544 (33%), Positives = 265/544 (48%), Gaps = 106/544 (19%) Query: 9 LQRLGRALMLPIAILPIAGLLL--------------RLGDTDLLDIAIIH---DAGQAIF 51 +QR G A+ P+ + P AG+++ L D L I+H + G +F Sbjct: 5 IQRFGGAMFTPVLLFPFAGIVVGIAIMLRNPMFVGEALTAPDSLFAQIVHIIEEGGWTVF 64 Query: 52 ANLAMIFAIGIAVGFARDNNGTAGLAGAIGY----------------------------- 82 N+ +IFA+G+ +G A+ G A LA + + Sbjct: 65 RNMPLIFAVGLPIGLAKQAQGRACLAVLVSFLTWNYFINAMGMTWGHFFGVDFSVEPTAG 124 Query: 83 --LVMIATLKVLDASINMGMLAGIISGLLAGALYNRFKDIKLPEYLAFFGGRRFVPIVTG 140 L M+A +K LD SI + A +ISGL+ AL+NR+ D LP +L F G FV IV Sbjct: 125 SGLTMMAGIKTLDTSI---IGAIVISGLVT-ALHNRYFDKPLPVFLGIFQGSSFVVIVAF 180 Query: 141 FSAVGLGVVFGLIWPPIQQGINGFGALLMESGSFGAFVFGVFNRLLIVTGLHHILNNMAW 200 + + + L WP +Q GI A L +G+ G +V+ R+LI TGLHH + Sbjct: 181 LAMIPCAWLTLLGWPKVQMGIESLQAFLRSAGALGVWVYIFLERILIPTGLHHFVYGP-- 238 Query: 201 FIFGSFTDPATGAVVTGDLSRYFAGD---------------PKGGQFMTGMFPVMLFGLP 245 FIFG AVV G + Y+A P+GG + G V FG Sbjct: 239 FIFGP-------AVVEGGIQVYWAQHLQAFSQSTEALKTLFPEGGFALHGNSKV--FGSV 289 Query: 246 AACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPLLFLVHALLTGVS 305 LA+Y A P+ R + G+L+ LT+ L G+TEP+EF F+F++PLLF VHA+L Sbjct: 290 GIALALYFTAAPENRVKVAGLLIPATLTAMLVGITEPLEFTFLFISPLLFAVHAVLAATM 349 Query: 306 MAVTNLLGIHLGFTFSGGFIDMVL--GW-----GKSTNGWLVVPVGLAYAAIYYLVFDFC 358 V + G+ +G F GG +D L W ++ ++ + VG+ + A+Y+++F Sbjct: 350 ATVMYICGV-VG-NFGGGLLDQFLPQNWIPMFHNHASMMFIQIGVGVCFTALYFVIFRTL 407 Query: 359 IRRFDLKTPGREE-----------VPAGDKPAIA-----ENQRAAAYIQALGGADNLITI 402 I R +LKTPGREE A K + A + +AA ++QALGGA N+ +I Sbjct: 408 ILRLNLKTPGREESEIKLYSKADYQAARGKTSAAGAADTKLGQAAGFLQALGGAGNIESI 467 Query: 403 GACTTRLRLDMVDRNKA-SDAQLKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAVP 461 C TRLR+ +VD K SD KALGA VVR GNG +QV+VG + D++ + Sbjct: 468 NNCATRLRIALVDMAKTQSDDVFKALGAHGVVRRGNG--IQVIVGLHVPQVRDQLETLMK 525 Query: 462 SSLR 465 SL+ Sbjct: 526 DSLQ 529 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: 711 Number of extensions: 30 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 571 Length of database: 540 Length adjustment: 36 Effective length of query: 535 Effective length of database: 504 Effective search space: 269640 Effective search space used: 269640 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: 53 (25.0 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