Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_011383691.1 AMB_RS06500 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000009985.1:WP_011383691.1 Length = 607 Score = 141 bits (355), Expect = 5e-38 Identities = 107/357 (29%), Positives = 177/357 (49%), Gaps = 31/357 (8%) Query: 10 LGTLMEREAAEAGAAVSRMLAANRD-AIERVAARLRASPPAVVVTCARGSSDHAATYAKY 68 L + E+ + A + + A+R + R+ L A ++ C G+S +A + AKY Sbjct: 253 LKEIFEQPEVVSNALNTMLNPADRTITLPRLPFDLAAVKRVRIIAC--GTSFYAGSVAKY 310 Query: 69 LIETLTGVPTASAALSVAS--LYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAFV 126 IE L +P + +AS Y P +GL + ISQSG++ D LA + + R+ G Sbjct: 311 WIEKLARLPVE---VDIASEFRYRCPPMEADGLAIFISQSGETADTLAALRYCREHGQHT 367 Query: 127 VAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALV--------AAWAQD 178 +++VN +S +A ++ + AGPE VA+TK++ L +A L A A+ Sbjct: 368 LSLVNVPESTIARESEAALLTMAGPEIGVASTKAFTTQLTVLACLAIGMGRATGALSAEA 427 Query: 179 EA-LETAVADLPAQLERAFALDWSAAVTA--LTGASGLFVLGRGYGYGIAQEAALKFKET 235 EA + +++++PA++ D V A + A + LGRG GY IA E ALK KE Sbjct: 428 EADICRSLSEIPARIAEVLRRDDDIRVIAQGIAEARDVLYLGRGTGYPIALEGALKLKEI 487 Query: 236 CALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVL----- 290 +HAE+++A E++HGP+A++ ++ V+ +D E V E +RG V+ Sbjct: 488 SYIHAEAYAAGELKHGPIALIDDSVPVIVICPTDELYEKTASNVQEVVARGGRVVFFSDR 547 Query: 291 -----LADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 L+ LP++ P + PIL +A +A+A+G D D P +L K Sbjct: 548 EGIDRLSAKVFSSMALPSV--DPVVAPILYAIPVQLLAYHVAVAKGTDVDQPRNLAK 602 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: 403 Number of extensions: 18 Number of successful extensions: 4 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: 607 Length adjustment: 33 Effective length of query: 314 Effective length of database: 574 Effective search space: 180236 Effective search space used: 180236 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 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