Align D-galactosamine-6-phosphate deaminase AgaS; GalN-6-P deaminase; Glucosamine-6-phosphate deaminase; GlcN-6-P deaminase; EC 3.5.99.-; EC 3.5.99.6 (characterized)
to candidate Echvi_0158 Echvi_0158 Predicted phosphosugar isomerases
Query= SwissProt::A0KYQ7 (386 letters) >FitnessBrowser__Cola:Echvi_0158 Length = 390 Score = 268 bits (686), Expect = 1e-76 Identities = 154/384 (40%), Positives = 229/384 (59%), Gaps = 20/384 (5%) Query: 16 LLLSAEQLTQYGAFWTAKEISQQPKMWRKVSEQ-HSDNRTIAAWLTPILAKPQLRIILTG 74 L L +E+ + GAF TAKEI+ QP++W++V Q ++ I +++ PIL K RI+LTG Sbjct: 7 LTLDSEKAEELGAFHTAKEIAGQPELWQRVFRQLKNEQNAIHSFIKPILEKGNARIVLTG 66 Query: 75 AGTSAYIGDVLAAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSP 134 AG+SA+IG+ +QQ + TQ AI+TTD+V+HPEL+ +PTLL+S+ RSGNSP Sbjct: 67 AGSSAFIGESAQGIVQQLTGVHTQ---AIATTDVVTHPELFFLEKVPTLLVSFARSGNSP 123 Query: 135 ESMAAVELAEQLVDDCYHLAITCNGQGKLANYCAD-KSHCYLYKLPDETHDVSFAMTSSF 193 ES+ AV LA+ ++ YHL ITCN G+LA Y D +C LP+ ++D S AMT SF Sbjct: 124 ESVEAVRLADAHCNEIYHLIITCNPDGELAAYANDCGGNCLALVLPEGSNDNSLAMTGSF 183 Query: 194 TCMYLATLLIFAPN-----SQALMQCIEMAEHILTERLADIRLQSEQPSKRVVFLGGGPL 248 T M LA LL+ + Q E A HIL L + ++ RV+FLG G + Sbjct: 184 TSMLLAILLVAGIDQLDQLKQQFEDAAETANHILRNSLHEFEAVAKSDFNRVIFLGSGAM 243 Query: 249 KAIAQEAALKYLELTAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDL 308 +A+E LK ELT G+VV +S LGFRHGP+++ + + V+ + S DP+ +Y+ DL Sbjct: 244 LGVARECHLKLQELTDGKVVCKHDSFLGFRHGPRAVANEESIVVYLFSRDPHVVRYETDL 303 Query: 309 IQELKRDNQALSVLTLSEELLTG--------SSGLNE--VWLGLPFILWCQILAIYKAIQ 358 + + D + + ++ + E G + G +E ++ LP + Q+L YK +Q Sbjct: 304 AKSIGEDKRKIRTISFAAENTDGYHSILDLPAVGTSEKAIFNVLPATMVGQLLGFYKCLQ 363 Query: 359 LKVSPDNPCPTGQVNRVVQGVNVY 382 L + PDNP +G ++RVVQGV +Y Sbjct: 364 LGLHPDNPSVSGAISRVVQGVTIY 387 Lambda K H 0.319 0.133 0.392 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: 336 Number of extensions: 16 Number of successful extensions: 6 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: 386 Length of database: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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: 50 (23.9 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