Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 340 bits (872), Expect = 1e-97 Identities = 203/518 (39%), Positives = 294/518 (56%), Gaps = 42/518 (8%) Query: 3 KALFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMES 62 + + LQ +GRALMLP+A+LP AG+LL IG D++ + + + Sbjct: 2 RKILETLQPLGRALMLPIAVLPVAGLLLRIGQP----DLLDI-------------AFVSA 44 Query: 63 AGQIVFDNLPLLFAVGVAIGLA-NGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVE 121 AG +F NL +LFA+GVA+G A +G+G A +A + YLV L+A + + + Sbjct: 45 AGTAIFGNLGILFAIGVAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPD 104 Query: 122 RAKFFTENHPA--YVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKR 179 A A ++ L +P GII G++ +NRF TI LP+YL FF G+R Sbjct: 105 AAAKVVAQAWATGQIDRLEVPI-------GIISGLIGGKFYNRFATIALPEYLAFFGGRR 157 Query: 180 FVPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLH 239 FVPI I+ L+L ++ + I L+A S +VE+ F++GV+ R L+ GLH Sbjct: 158 FVPIAAGIAGLLLAGVLGYGYAHISSALDAASHAVVESGGA-GMFVYGVLNRLLLVTGLH 216 Query: 240 HIFYSPFWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAA 299 H+ + W+ + A G++ R F A + AG FM+G +P MMFGLPAA Sbjct: 217 HLLNNVAWFLVGDFGGATGDLGR-----FFAGDPN-----AGAFMSGFFPVMMFGLPAAC 266 Query: 300 LAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMV 359 LA+YHEA+P+ +K V G++ S A TSFLTG+TEP+EF+F+F+APVL+AIH + G++ + Sbjct: 267 LAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTL 326 Query: 360 MQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKT 419 M +L +K+G FS GL DY L L R W+++PVG AVIYY FRF IRK +L T Sbjct: 327 MDMLGIKLGFGFSAGLFDYVLNFKLSTRP--WMLLPVGAAYAVIYYTLFRFFIRKLDLAT 384 Query: 420 PGREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDR 479 PGRE E AA G+T + ++A+G N+ +DAC TRLR+ V DQ VD Sbjct: 385 PGRE-KGEAVAAAGETAAGNERGAAFVKALGGAANLTSVDACTTRLRLIVADQSAVDDAA 443 Query: 480 LKQLGASGVLE-VGNNIQAIFGPRSDGLKTQMQDIIAG 516 L LGA G++ N Q + GP +D + +++ I G Sbjct: 444 LNALGARGIIRPSANATQVVLGPIADLVAEEIRGAIGG 481 Score = 35.4 bits (80), Expect = 7e-06 Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 2/58 (3%) Query: 425 AAEETAAPGKT--GEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRL 480 AA +AAP + EA LP IL A+G + NI+ L A R RV V D + D+ L Sbjct: 483 AAAVSAAPAQALADEAVTLPAAILAALGGEANIRALQALHGRFRVEVVDAARTDEASL 540 Lambda K H 0.323 0.141 0.412 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: 1051 Number of extensions: 67 Number of successful extensions: 9 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: 699 Length of database: 560 Length adjustment: 38 Effective length of query: 661 Effective length of database: 522 Effective search space: 345042 Effective search space used: 345042 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 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