Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_028311942.1 H566_RS0114125 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000482785.1:WP_028311942.1 Length = 608 Score = 124 bits (311), Expect = 6e-33 Identities = 111/357 (31%), Positives = 164/357 (45%), Gaps = 34/357 (9%) Query: 14 MEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAV--------VVTCARGSSDHAATY 65 M++E E A+ L A+ER+ L P V+ A G+S +A Sbjct: 253 MQKEIFEQPRAIGDTL----QAVERIGPELLGLAPDAEPFKGIERVLILACGTSYYAGCV 308 Query: 66 AKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAF 125 A+Y +E++ VP S D P L + ISQSG++ D LA + + G Sbjct: 309 ARYWLESIARVPCNVEVASEFRYRDPATDPAT-LVVVISQSGETADTLAALREAQSLGMT 367 Query: 126 -VVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQ-----DE 179 +A+ N S + + +AG E VA+TK++ L + L +A+ D Sbjct: 368 QTLAVCNVATSTMVRETSLQFITRAGVEIGVASTKAFTTQLVGLYLLTLLFAKARGRLDA 427 Query: 180 ALET----AVADLPAQLERAFALDWSAAVTALTGA---SGLFVLGRGYGYGIAQEAALKF 232 A E A+ LPA ++ AL+ A A + LF LGRG Y IA E ALK Sbjct: 428 AAEAEALKALRHLPAAVQSVVALEPQIIAWAEQFARKENALF-LGRGMHYPIALEGALKL 486 Query: 233 KETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLA 292 KE +HAE++ A E++HGP+A+V A V+ A +D E ++ + E R+RG E+ + Sbjct: 487 KEISYIHAEAYPAGELKHGPLALVTAAMPVVTVAPNDALVEKLKSNMQEVRARGGELYVF 546 Query: 293 DPAARQ----AGLPAIAA---HPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 A Q G+ I + A+ PIL V +A A ARG D D P +L K Sbjct: 547 ADAGTQIESSEGVHVIRMPEHYGALSPILHVVPLQLLAYHTATARGTDVDKPRNLAK 603 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: 413 Number of extensions: 15 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: 608 Length adjustment: 33 Effective length of query: 314 Effective length of database: 575 Effective search space: 180550 Effective search space used: 180550 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 24 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