Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate BPHYT_RS23405 BPHYT_RS23405 glucosamine--fructose-6-phosphate aminotransferase
Query= reanno::Korea:Ga0059261_1644 (347 letters) >FitnessBrowser__BFirm:BPHYT_RS23405 Length = 605 Score = 117 bits (292), Expect = 1e-30 Identities = 110/361 (30%), Positives = 163/361 (45%), Gaps = 43/361 (11%) Query: 14 MEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCAR------GSSDHAATYAK 67 M++E E AVS+ N A + A+ A+ P R G+S ++A AK Sbjct: 251 MQKEIFEQPLAVSKTFPRN-SAFD--ASLFGATDPQAFAQIDRILLLGCGTSHYSALTAK 307 Query: 68 YLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGA-FV 126 E++ +PT +S Y + N L + ISQSG++ D L + H + G Sbjct: 308 AWFESIAKIPT-QVEISSEYRYRETIPGKNTLVVPISQSGETADTLGALMHAQSLGQDHT 366 Query: 127 VAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEALETAVA 186 +A+ N S + + +AGPE VA+TK++ L A+ L L A Sbjct: 367 LAICNVATSAIVRQSRWSFITQAGPEIGVASTKAFTTQLVALFVLAVT------LGRARG 420 Query: 187 DLPAQLERAFALDWSAAVTALTGA------------------SGLFVLGRGYGYGIAQEA 228 + AQ E ++ S TAL G S +F LGRG + IA E Sbjct: 421 YVDAQQEASYRSQLSGLSTALQGVLAREPQIIAWAHEIARTDSAIF-LGRGSHFPIALEG 479 Query: 229 ALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAE 288 ALK KE +HAE + A E++HGP+A+V +A V+ A +D E ++ + E R+R + Sbjct: 480 ALKLKEISYIHAEGYPAGELKHGPLALVTDAMPVVVTAPNDGLLEKLKSNIQEVRARRGQ 539 Query: 289 V-LLADPAA---RQAGLPAIAA---HPAIEPILIVQSFYKMANALALARGCDPDSPPHLN 341 V + AD A + GL I + A+ PIL V +A A RG D D P +L Sbjct: 540 VYVFADADANLSNEEGLRVIQMPEYYGALSPILHVLPLQLLAYHTACTRGTDVDKPRNLA 599 Query: 342 K 342 K Sbjct: 600 K 600 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: 398 Number of extensions: 17 Number of successful extensions: 4 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: 605 Length adjustment: 33 Effective length of query: 314 Effective length of database: 572 Effective search space: 179608 Effective search space used: 179608 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