Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_086511382.1 BZY95_RS18595 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_002151265.1:WP_086511382.1 Length = 616 Score = 138 bits (348), Expect = 3e-37 Identities = 118/358 (32%), Positives = 168/358 (46%), Gaps = 29/358 (8%) Query: 10 LGTLMEREAAEAGAAVSRMLAANRDAIERVAARLRA--SPPAVVVTCARGSSDHAATYAK 67 L + E+ A A A R L ++R +E R RA + A G+S HAA A+ Sbjct: 258 LKEIHEQPVAVANALEGR-LGSDRVLVEAFGPRARALLGEARQIHLVACGTSYHAAMVAR 316 Query: 68 YLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKA----- 122 Y IE+L GVP S D PG L L +SQSG++ D LA + H RK Sbjct: 317 YWIESLAGVPCQVEIASEYRYRDVATPPGT-LLLTLSQSGETADTLAALRHARKQRPDRY 375 Query: 123 -GAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQ---- 177 GA +++ N S L +D+ + AGPE VA+TK++ L A+ + Q Sbjct: 376 IGA--LSICNVPGSSLVRESDLSLMTHAGPEIGVASTKAFTTQLTALMLVALGLRQLRGG 433 Query: 178 DEALETAVAD----LPAQLERAFALDWSAAVTA--LTGASGLFVLGRGYGYGIAQEAALK 231 DE L V LP L L+ A A LGRG IA E ALK Sbjct: 434 DEELTARVVHHLRYLPTLLGDTLKLEGEIASLAKRFCDYRHTLFLGRGAQMPIAMEGALK 493 Query: 232 FKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLL 291 KE +HAE+++A E++HGP+A++ + V+A A D E ++ +AE R+RG ++L+ Sbjct: 494 LKEISYIHAEAYAAGELKHGPLALIDASMPVVALAPKDELLEKLKSNLAEVRARGGQLLV 553 Query: 292 -ADPAA--RQAGLPAIAAHPA----IEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 ADP + Q + P + PI +A +A+ARG D D P +L K Sbjct: 554 FADPESGLEQGDGMTVVKVPGCCRFLAPIAYTVPLQLLAYHVAVARGTDVDQPRNLAK 611 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: 446 Number of extensions: 21 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: 616 Length adjustment: 33 Effective length of query: 314 Effective length of database: 583 Effective search space: 183062 Effective search space used: 183062 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