Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Korea:Ga0059261_1647 Length = 560 Score = 440 bits (1132), Expect = e-128 Identities = 219/476 (46%), Positives = 307/476 (64%), Gaps = 25/476 (5%) Query: 1 MLSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAI 60 +L LQ LG++ MLPIAVLP G++L +G+ D+ +I FV AGTA+F +L ++FAIG+A+ Sbjct: 4 ILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGVAV 63 Query: 61 GISKDSNGAAGLSGAISYLML-------------------DAATKTIDKT------NNMA 95 G ++D NGAA L+G YL+ DAA K + + + + Sbjct: 64 GFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQAWATGQIDRLE 123 Query: 96 VFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQS 155 V GII+GLI G YNRF LPEYL FF GRR VPI I ++LAG+ G + I S Sbjct: 124 VPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGYGYAHISS 183 Query: 156 CINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTGDLARFFAK 215 +++ ++ GG G ++G+ NRLL+ GLHH+LNN+ WF G++ G TGDL RFFA Sbjct: 184 ALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDFGGATGDLGRFFAG 243 Query: 216 DPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEF 275 DP AG +M+GFFP+MMFGLPAACLAM A+P +RKA GM+ A T+F+TG+TEPIEF Sbjct: 244 DPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAFTSFLTGVTEPIEF 303 Query: 276 AFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGI 335 FMFL+P+LYA+HAVLTG+++ +++ LGI+ GF FSAG DYVL++ ++ +P +LL VG Sbjct: 304 TFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFKLSTRPWMLLPVGA 363 Query: 336 CYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTID 395 YA +Y+ +F I+ L+L TPGRE + E + +K LGG NL ++D Sbjct: 364 AYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFVKALGGAANLTSVD 423 Query: 396 HCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451 C TRLRL V D + VD+A L GA+G+++ + QV++GP + AEE+R A+ Sbjct: 424 ACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIADLVAEEIRGAI 479 Score = 29.6 bits (65), Expect = 3e-04 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%) Query: 381 MLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVV 425 +L LGG+ N++ + R R+ V D A DEA L A A G V Sbjct: 505 ILAALGGEANIRALQALHGRFRVEVVDAARTDEASL-LAAANGAV 548 Lambda K H 0.326 0.144 0.429 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: 691 Number of extensions: 41 Number of successful extensions: 3 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: 452 Length of database: 560 Length adjustment: 34 Effective length of query: 418 Effective length of database: 526 Effective search space: 219868 Effective search space used: 219868 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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