Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate RR42_RS09880 RR42_RS09880 glucosamine--fructose-6-phosphate aminotransferase
Query= reanno::Korea:Ga0059261_1644 (347 letters) >FitnessBrowser__Cup4G11:RR42_RS09880 Length = 501 Score = 132 bits (332), Expect = 2e-35 Identities = 106/314 (33%), Positives = 156/314 (49%), Gaps = 26/314 (8%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110 V+ A G+S H+ AKY +E+++ +PT+ S D+ P L LAISQSG++ Sbjct: 187 VLILACGTSYHSGMTAKYWLESISRLPTSVEIASEYRYRDSVPNPRT-LVLAISQSGETA 245 Query: 111 DLLATVEHQRKAG-AFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIA 169 D LA ++H + G +A+ N S + A + +AG E VA+TK++ L A+ Sbjct: 246 DTLAALKHAQVLGHRHTLAVCNVAGSAILRQAALHFLTRAGAEIGVASTKAFTTQLVALF 305 Query: 170 ALVAAWAQ---------DEALETAVADLPAQLERAFALD-----WSAAVTALTGASGLFV 215 L A A+ + A+ + LPA L AL W+ ++ A Sbjct: 306 VLAATLAKRRGMLDAHREAAMLGQLHHLPAALNGVLALAPQIIAWAGSLARKENA---LF 362 Query: 216 LGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESV 275 LGRG Y IA E ALK KE +HAE+++A E++HGP+A+V E V+ A +D E + Sbjct: 363 LGRGIHYPIALEGALKLKEISYIHAEAYAAGELKHGPLALVTEQMPVVTVAPNDALLEKL 422 Query: 276 RETVAEFRSRGAEVLL---ADPAARQA-GLPAIAA---HPAIEPILIVQSFYKMANALAL 328 + + E R+RG E+ + AD R A GL I + + PIL V +A A Sbjct: 423 KSNLQEVRARGGELYVFSDADSKIRSAPGLHVIRMPEHYGLLSPILHVVPLQLLAYHTAC 482 Query: 329 ARGCDPDSPPHLNK 342 ARG D D P L K Sbjct: 483 ARGTDVDKPRDLAK 496 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: 337 Number of extensions: 24 Number of successful extensions: 5 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: 501 Length adjustment: 31 Effective length of query: 316 Effective length of database: 470 Effective search space: 148520 Effective search space used: 148520 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: 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