Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate 1937101 b3718 hypothetical protein (NCBI)
Query= curated2:Q8ESL6 (250 letters) >FitnessBrowser__Keio:1937101 Length = 240 Score = 126 bits (317), Expect = 3e-34 Identities = 79/251 (31%), Positives = 139/251 (55%), Gaps = 22/251 (8%) Query: 1 MKIIQTENYQSMSKLASQHVINTIKQLNKPVLGLATGSTPEGLYQHLIKAYRMHQISFAN 60 MK+I TE+YQ MS++A+ H++ + + + L + GSTP+G+Y++L + + + N Sbjct: 1 MKLIITEDYQEMSRVAAHHLLGYMSKTRRVNLAITAGSTPKGMYEYLTTLVK-GKPWYDN 59 Query: 61 VSTFNLDEYVGLHKEDKNSYHYYMQKFLFNHVDIPYKNIHLPNGIAKDLSVE-CTSYEDR 119 +N DE KE + ++ F I +NI + L+++ ++ + Sbjct: 60 CYFYNFDEIPFRGKEGEGVTITNLRNLFFTPAGIKEENI-------QKLTIDNYREHDQK 112 Query: 120 IQQAGGIHIQVLGIGRNGHIGFNEPGTS--------FESQTHVVDLDESTRNANARFFDS 171 + + GG+ + VLG+G +GH N P T+ F Q +VD+ A+ Sbjct: 113 LAREGGLDLVVLGLGADGHFCGNLPNTTHFHEQTVEFPIQGEMVDIV-----AHGELGGD 167 Query: 172 IDEVPNQAITMGIQSIMRAKEILLLVSGSEKAEALEKLVNGNVSEEFPASILQTHQNVKI 231 VP+ +TMG +SIM AK +L++VSG+ KA+AL+ ++ G V+E+ PAS+LQ H ++ + Sbjct: 168 FSLVPDSYVTMGPKSIMAAKNLLIIVSGAGKAQALKNVLQGPVTEDVPASVLQLHPSLMV 227 Query: 232 IADKAALQDIS 242 IADKAA +++ Sbjct: 228 IADKAAAAELA 238 Lambda K H 0.317 0.132 0.372 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: 158 Number of extensions: 9 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: 250 Length of database: 240 Length adjustment: 24 Effective length of query: 226 Effective length of database: 216 Effective search space: 48816 Effective search space used: 48816 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: 41 (21.6 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