Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_028951259.1 Q385_RS0108520 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000619805.1:WP_028951259.1 Length = 604 Score = 112 bits (281), Expect = 2e-29 Identities = 97/311 (31%), Positives = 137/311 (44%), Gaps = 20/311 (6%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110 +V A G+S HA K+ IE VPT S D P+ L +AISQSG++ Sbjct: 290 IVIIACGTSYHAGLVGKFWIEKFVKVPTIVDYASEFRYRDFPINEKT-LIIAISQSGETA 348 Query: 111 DLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAI-- 168 D + RK GA V+++VN S L+ +D VI GPE VAATK++ L + Sbjct: 349 DTRFSAIDARKKGAKVLSIVNVVGSSLSRESDFVIYTYCGPEIGVAATKTFTAQLITLLL 408 Query: 169 ----AALVAAWAQDEALE---TAVADLPAQLERAFALDWSAAVTALT--GASGLFVLGRG 219 A L E E V LP + D + LGRG Sbjct: 409 FSLKAGLERGNLTQEEFEKYHNDVIHLPHLINEVLKQDKVIEEISYKYHNVKDFLFLGRG 468 Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279 Y IA E ALK KE +HAE + A E++HGP+A++ E V+ D E + + Sbjct: 469 LNYPIALEGALKLKEISYIHAEGYPAGEMKHGPIALIDENLPVVCMVPKDSLYEKMISNI 528 Query: 280 AEFRSR-GAEVLLADPAARQAGLP--AIAAHPAIE-----PILIVQSFYKMANALALARG 331 E ++R G + ++D P +I P++E PI+ V +A +A G Sbjct: 529 QEVKARKGIVISISDSQDSHLLSPSDSIIKIPSVENENLYPIISVVPLQLLAYHIATILG 588 Query: 332 CDPDSPPHLNK 342 D D P +L K Sbjct: 589 KDVDQPRNLAK 599 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: 333 Number of extensions: 11 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: 604 Length adjustment: 33 Effective length of query: 314 Effective length of database: 571 Effective search space: 179294 Effective search space used: 179294 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