Align N-acetylgalactosamine kinase AgaK; GalNAc kinase; N-acetylglucosamine kinase; GlcNAc kinase; EC 2.7.1.-; EC 2.7.1.59 (characterized)
to candidate SMc02880 SMc02880 hypothetical protein
Query= SwissProt::A0KYQ6 (308 letters) >FitnessBrowser__Smeli:SMc02880 Length = 303 Score = 161 bits (407), Expect = 2e-44 Identities = 100/298 (33%), Positives = 156/298 (52%), Gaps = 8/298 (2%) Query: 6 DIGGTKIELAIFDTQLALQDKWRLSTPGQDYSAFMATLAEQIEKADQQCGERGTVGIALP 65 DIGG+ I+ AI + + R +TP D+ F+ + +++A G V I++ Sbjct: 6 DIGGSAIKGAITHSPERIFPLPRRATPLTDFGRFVEAMESVLDEAG---GLPERVAISIT 62 Query: 66 GVVKADGTVIS-SNVPCLNQRRVAHDLAQLLNRTVAIGNDCRCFALSEAVLGVGRGYSRV 124 GV+ + I +N+PC++ R + +L L+ V I ND CFAL+EA +G GRG+ V Sbjct: 63 GVIDPETRRIKCANIPCIDGRELVAELEAALHLPVVIANDADCFALAEAGVGAGRGHRIV 122 Query: 125 LGMILGTGTGGGLCIDGKLYLGANRLAGEFGHQGVSANVACRH---QLPLYVCGCGLEGC 181 G ILGTG GGGL IDG+L AGE+GH G + A H +P + CGCG C Sbjct: 123 FGAILGTGVGGGLVIDGRLINADGGFAGEWGH-GPAVAAAAGHPPIAIPAFPCGCGQSRC 181 Query: 182 AETYVSGTGLGRLYQDIAGQTADTFAWLNALRCNDPLAIKTFDTYMDILGSLMASLVLAM 241 +T GL RL++ + G+ + + + + A +T D ++D++ S +A ++ Sbjct: 182 VDTVGGARGLERLHETVHGKALSSHDIIEGWQNGNAEAARTIDVFVDLVSSPLALVINIT 241 Query: 242 DPDIIVLGGGLSEVEEILAALPQATKAHLFDGVTLPQFKLADFGSASGVRGAALLGHG 299 I+ +GGGLS E +LA + +A +A + P + G+ GAALLG G Sbjct: 242 GATIVPVGGGLSNAEALLAEIDRAVRARILRRFDRPLVVRGECRVEPGLIGAALLGFG 299 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: 275 Number of extensions: 17 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: 303 Length adjustment: 27 Effective length of query: 281 Effective length of database: 276 Effective search space: 77556 Effective search space used: 77556 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