Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 208675 DVU3156 glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >MicrobesOnline__882:208675 Length = 607 Score = 124 bits (312), Expect = 5e-33 Identities = 112/356 (31%), Positives = 167/356 (46%), Gaps = 36/356 (10%) Query: 14 MEREAAEAGAAVSRMLAANRD-AIERVAARLRASPPAV----VVTCARGSSDHAATYAKY 68 M +E E V+ LA D A E V A+ P +V C G+S HA + K+ Sbjct: 256 MLKEIFEQPKVVTDCLAGRVDWAREEVTLPELAALPVPKRLHIVAC--GTSLHAGMWGKH 313 Query: 69 LIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAFVVA 128 L+E+ VP + S D + P + + L ISQSG++ D LA + R+ G V Sbjct: 314 LLESWAKVPVSVEIASEFRYRDILLDPED-MVLVISQSGETADTLAGLRIAREKGVKVAG 372 Query: 129 MVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEALE------ 182 + N S +A AD VI +AGPE SVA+TK+ + + L W + +A Sbjct: 373 LCNVVGSSIAREADAVIYTQAGPEISVASTKAMCSQMVLLTLLALYWGRRKATLADDVRH 432 Query: 183 ---TAVADLPAQLERAF-ALDWSAAVTALT--GASGLFVLGRGYGYGIAQEAALKFKETC 236 +A+ LP QLE A + A A T A F LGRG+ + +A E ALK KE Sbjct: 433 EALSALRKLPGQLESALPGMRDEAQQLARTYSKARSFFYLGRGHCFPLALEGALKLKEIS 492 Query: 237 ALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSR----------G 286 +HAE +++ E++HGP+A++ F A A +D V+ + E ++R G Sbjct: 493 YIHAEGYASGEMKHGPIALIDPEFPTFALALADDLFPKVKSNIEEVQARRGKVIALTNPG 552 Query: 287 AEVLLADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 EV + +P A +AA A+ + + Y+ A+ L G D D P +L K Sbjct: 553 VEVRVDNPWVVPAAWGPLAAFIALPALQLFS--YEAADYL----GKDVDQPRNLAK 602 Lambda K H 0.317 0.128 0.360 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: 415 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: 347 Length of database: 607 Length adjustment: 33 Effective length of query: 314 Effective length of database: 574 Effective search space: 180236 Effective search space used: 180236 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 (21.7 bits) S2: 51 (24.3 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