Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_012050727.1 SWIT_RS22990 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000016765.1:WP_012050727.1 Length = 608 Score = 162 bits (409), Expect = 3e-44 Identities = 111/313 (35%), Positives = 162/313 (51%), Gaps = 26/313 (8%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVAS--LYDAPVAPGNGLCLAISQSGK 108 +V C G+S +A AKY E VP L VAS Y PV GL L ISQSG+ Sbjct: 296 IVAC--GTSFYAGMVAKYWFEQFARVPVD---LDVASEFRYREPVMEDGGLALFISQSGE 350 Query: 109 SPDLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAI 168 + D LA + H R G + +VN S +A AD+++P AGPE VA+TK++ C LA + Sbjct: 351 TADTLAALRHARSEGQKIAVVVNVPTSTMAREADLLLPTHAGPEIGVASTKAFTCQLAVL 410 Query: 169 AALVAAWAQ---------DEALETAVADLPAQLERAFALDWS--AAVTALTGASGLFVLG 217 AAL A A+ ++ + +++ PA + A A D S A + + GA + LG Sbjct: 411 AALAANLARAKGRLDAKAEKEIVRHLSEAPAAINGALAYDESIEAMASVIAGARDVLYLG 470 Query: 218 RGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRE 277 RG Y +A E ALK KE +HAE ++A E++HGP+A++ E V+ A S + Sbjct: 471 RGPDYPLALEGALKLKEISYIHAEGYAAGEMKHGPIALIDENVPVIVIAPSGPLFDKTVS 530 Query: 278 TVAEFRSRGAEVLLAD--PAARQAGLPAIA------AHPAIEPILIVQSFYKMANALALA 329 + E ++RG +V+L + AG +A HP I PI+ +A +A+A Sbjct: 531 NMQEVQARGGKVVLISDYDGIQAAGENCMATITMPKVHPLIAPIVYAIPVQLLAYHVAVA 590 Query: 330 RGCDPDSPPHLNK 342 +G D D P +L K Sbjct: 591 KGTDVDQPRNLAK 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: 417 Number of extensions: 23 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: 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 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