Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_011610309.1 TERY_RS02150 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_000014265.1:WP_011610309.1 Length = 633 Score = 124 bits (312), Expect = 5e-33 Identities = 95/313 (30%), Positives = 152/313 (48%), Gaps = 26/313 (8%) Query: 55 ARGSSDHAATYAKYLIETLTGVPTASAALSVASLYDAPVAPGNGLCLAISQSGKSPDLLA 114 A G+S HA+ KYL+E L G+ T S A +P+ N L + ++QSG++ D LA Sbjct: 317 ACGTSWHASLIGKYLLEQLAGISTTVNYASEARYAPSPLR-ANTLTIGVTQSGETADTLA 375 Query: 115 T--VEHQRKAGAFV------VAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLA 166 +E QR+ V + + N +S +A+L +I ++AG E VAATK+++ + Sbjct: 376 ALAIEQQRRLDKPVEFTSRLLGITNRVESSIASLVHQIIDIRAGVEIGVAATKTFVAQVI 435 Query: 167 AI--AALVAAWAQDEALETAVADL-------PAQLERAFALDWSAA---VTALTGASGLF 214 A A+ W + +A++ PAQ+E+ S L Sbjct: 436 AFYFLAIDLGWQRKYLSGEKIAEIINGLQKIPAQMEQILDSQNSQIEDFAHQFNNTQDLI 495 Query: 215 VLGRGYGYGIAQEAALKFKETCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGES 274 +GRG Y IA E ALK KE +HAE + A E++HGP+A++ + V+A A E Sbjct: 496 FIGRGINYPIALEGALKLKEISYIHAEGYPAGEMKHGPIALLDDQVPVVAIAMPGLVYEK 555 Query: 275 VRETVAEFRSRGAEVLLADPAARQAGL-PAIAAHPAIE----PILIVQSFYKMANALALA 329 V E ++R A+++ P + + + + A PA++ P+L V +A +A Sbjct: 556 VLSNAQEAKARDAQLIGVTPESTEVDMFDNVLAVPAVDELLSPMLTVIPLQLLAYHIAAH 615 Query: 330 RGCDPDSPPHLNK 342 RG D D P +L K Sbjct: 616 RGLDVDQPRNLAK 628 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: 371 Number of extensions: 16 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: 633 Length adjustment: 33 Effective length of query: 314 Effective length of database: 600 Effective search space: 188400 Effective search space used: 188400 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