Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate 17214 b3141 galactosamine-6-phosphate isomerase (NCBI)
Query= curated2:Q890L6 (241 letters) >FitnessBrowser__Keio:17214 Length = 251 Score = 137 bits (345), Expect = 2e-37 Identities = 79/229 (34%), Positives = 127/229 (55%), Gaps = 5/229 (2%) Query: 7 DNYDELSEVAALEILELIDKKPDCVLGLATGSTPVGTYQKLIEYYKKGKVDFSKVTSFNL 66 +NY LSE A+ +L +I KP+ V+ LATG+TP+ TY L+E + +VD S++T L Sbjct: 26 ENYTALSERASEYLLAVIRSKPNAVICLATGATPLLTYHYLVEKIHQQQVDVSQLTFVKL 85 Query: 67 DEYRGLNGEHPQSYKFFMNNTLFNHINIDKKNTFILDGLSNDI-EKECIEYDKKIDNKGG 125 DE+ L P + + F+ + + + + ++ S +I E EC I KGG Sbjct: 86 DEWVDLPLTMPGTCETFLQQHIVQPLGLREDQ--LISFRSEEINETECERVTNLIARKGG 143 Query: 126 IDLQILGIGGNGHIGFNEPSEELSISTHLTKLKTKTIKDNSRFFNSEEEVPTEAITMGIG 185 +DL +LG+G NGH+G NEP E L + H+++L +T + T IT+G+ Sbjct: 144 LDLCVLGLGKNGHLGLNEPGESLQPACHISQLDART--QQHEMLKTAGRPVTRGITLGLK 201 Query: 186 SIMKARKIILLINGEVKAEIVKKLINGNVSTKVPASLLHLHPNCTVILD 234 I+ AR+++LL+ GE K + + + VST +PAS L LH N +++ Sbjct: 202 DILNAREVLLLVTGEGKQDATDRFLTAKVSTAIPASFLWLHSNFICLIN 250 Lambda K H 0.316 0.137 0.383 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: 101 Number of extensions: 3 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: 241 Length of database: 251 Length adjustment: 24 Effective length of query: 217 Effective length of database: 227 Effective search space: 49259 Effective search space used: 49259 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 46 (22.3 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