Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_041096967.1 SUTH_RS02960 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000828635.1:WP_041096967.1 Length = 609 Score = 132 bits (332), Expect = 2e-35 Identities = 102/314 (32%), Positives = 161/314 (51%), Gaps = 26/314 (8%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNG--LCLAISQSGK 108 V+ A G+S HA A+Y IE L G+ ++ +AS Y V+ N L +AISQSG+ Sbjct: 295 VLILACGTSFHAGLVARYWIEQLAGI---GCSVEIASEYRYRVSVPNPEQLVVAISQSGE 351 Query: 109 SPDLLATVEHQRKAG-AFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAA 167 + D LA+++H + G +A+ N +S + + +AGPE VA+TK++ LAA Sbjct: 352 TADTLASIKHAKALGMGRTLAICNVPESAIVRECALRFLTRAGPEIGVASTKAFTTQLAA 411 Query: 168 IAALVAAWAQDEALET---------AVADLPAQLERAFALDWSAAVTALTGAS---GLFV 215 + L A+ A+ LP +++ AL+ V A A LF Sbjct: 412 LFLLAVTLAKQNGRLAPEHEAGHLKALRHLPVAVQKVLALEPDIKVWATRFADKHHALF- 470 Query: 216 LGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESV 275 LGRG+ Y IA E ALK KE +HAE + A E++HGP+A+V + V++ A +D E + Sbjct: 471 LGRGHHYPIALEGALKLKEISYIHAEGYPAGELKHGPLALVDKDMPVISIAPNDALLEKL 530 Query: 276 RETVAEFRSRGAEVLL---ADPAA-RQAGLPAIAA---HPAIEPILIVQSFYKMANALAL 328 + + E +RG E+ + AD A +AG+ + + + P+L V + ++ AL Sbjct: 531 KSNLKEVAARGGELYVFADADSAVDEEAGVHVLRLPEHYGLLSPVLHVIALQLLSYHAAL 590 Query: 329 ARGCDPDSPPHLNK 342 +G D D P +L K Sbjct: 591 VKGTDVDKPRNLAK 604 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: 424 Number of extensions: 19 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: 609 Length adjustment: 33 Effective length of query: 314 Effective length of database: 576 Effective search space: 180864 Effective search space used: 180864 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 Apr 09 2024. 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