Align N-acetylgalactosamine kinase AgaK; GalNAc kinase; N-acetylglucosamine kinase; GlcNAc kinase; EC 2.7.1.-; EC 2.7.1.59 (characterized)
to candidate 6937023 Sama_1197 putative ROK-family protein (RefSeq)
Query= SwissProt::A0KYQ6 (308 letters) >FitnessBrowser__SB2B:6937023 Length = 335 Score = 375 bits (962), Expect = e-108 Identities = 187/312 (59%), Positives = 230/312 (73%), Gaps = 13/312 (4%) Query: 1 MYYGLDIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGE---- 56 M+YGLDIGGTKI LA+FD +A ++W++ TP DY F+ + QIE+AD+ + Sbjct: 1 MHYGLDIGGTKIALALFDDSMACVERWQIPTPVADYGQFLDEVCAQIERADELAQQHSGV 60 Query: 57 --------RGTVGIALPGVVKADGTVISSNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCF 108 +G+VGIALPGV+ +DGTV+SSNVPCLN R VA +L L R VA+GNDCRCF Sbjct: 61 TVQPAEVSKGSVGIALPGVILSDGTVLSSNVPCLNGRTVAQELTVRLGRPVALGNDCRCF 120 Query: 109 ALSEAVLGVGRGYSRVLGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGVSANVACRHQ 168 ALSE +LG G G+ RVLG+ILGTG GGG+CI KL LGA+ LAGEFGH G+ A+V +HQ Sbjct: 121 ALSEVLLGAGVGFERVLGVILGTGLGGGVCISQKLILGAHCLAGEFGHIGLPASVIIKHQ 180 Query: 169 LPLYVCGCGLEGCAETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMD 228 LPL+ CGCGL GCAETYVSGTGLGRLYQ G TADT+ WL R AI TFD YMD Sbjct: 181 LPLFECGCGLTGCAETYVSGTGLGRLYQHFGG-TADTYVWLADYRSGKAEAISTFDAYMD 239 Query: 229 ILGSLMASLVLAMDPDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSAS 288 LGS++A +L++DPD +V GGG+SEV+EI+AALP AT HLF LP+F++A+FG+AS Sbjct: 240 ALGSVLAGQILSLDPDCLVFGGGISEVKEIIAALPDATARHLFASAKLPEFRVAEFGAAS 299 Query: 289 GVRGAALLGHGL 300 GVRGAALLG L Sbjct: 300 GVRGAALLGKAL 311 Lambda K H 0.321 0.140 0.421 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: 402 Number of extensions: 21 Number of successful extensions: 3 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: 308 Length of database: 335 Length adjustment: 28 Effective length of query: 280 Effective length of database: 307 Effective search space: 85960 Effective search space used: 85960 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: 48 (23.1 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