Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate AZOBR_RS09675 AZOBR_RS09675 glucosamine--fructose-6-phosphate aminotransferase
Query= reanno::Korea:Ga0059261_1644 (347 letters) >FitnessBrowser__azobra:AZOBR_RS09675 Length = 608 Score = 132 bits (332), Expect = 2e-35 Identities = 97/313 (30%), Positives = 153/313 (48%), Gaps = 26/313 (8%) Query: 51 VVTCARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSP 110 +V C G++ +A AKY ETL +P S +AP+ P G+ L ISQSG++ Sbjct: 296 IVAC--GTAYYAGVVAKYWFETLARLPVEVDIASEFRYREAPL-PEGGVALFISQSGETL 352 Query: 111 DLLATVEHQRKAGAFVVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAA 170 D L + + ++ G ++++VN +S +A +D V+ AGPE VA+TK++ L +A Sbjct: 353 DTLEALRYCKRQGQKILSIVNVPESTIARESDAVLYTMAGPEIGVASTKAFTTQLTTLAC 412 Query: 171 L---------VAAWAQDEALETAVADLPAQLERAFALDWSAAVTA--LTGASGLFVLGRG 219 L V + + + A+ ++PA+ A D A + A + LGRG Sbjct: 413 LAVTVGHARGVIPAERMQQIAQALREVPARAADVLAHDERLHELAQEVAEARDVLYLGRG 472 Query: 220 YGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETV 279 Y +A E ALK KE +HAE ++A E++HGP+A++ E+ V+ SD E V Sbjct: 473 AMYPLALEGALKLKEISYIHAEGYAAGELKHGPIALIDESVPVIVLVPSDNLFEKTVSNV 532 Query: 280 AEFRSRGAEVL----------LADPAARQAGLPAIAAHPAIEPILIVQSFYKMANALALA 329 E +R +VL L+D LP A P + P+L +A +A+ Sbjct: 533 QEVCARSGKVLLIADKKGIDKLSDKVRWSLELP--ACDPLVAPLLYAIPVQLLAYHVAVL 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: 398 Number of extensions: 23 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: 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 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