Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_072783034.1 BUA36_RS07360 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_900143065.1:WP_072783034.1 Length = 609 Score = 130 bits (326), Expect = 1e-34 Identities = 113/368 (30%), Positives = 171/368 (46%), Gaps = 26/368 (7%) Query: 13 APTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQAL----AQRLRANPPRVVVT 68 A TGA+ L P +M +E E RV L + L A + RV++ Sbjct: 241 AHTGAA--ELGPYRHYMQKEIFEQPRVIGDTLEGVTGIMPELFGDGAYNVFKQIDRVLIL 298 Query: 69 CARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLL 128 A G+S ++ A+Y IE+ A + + S D+ P+ L + ISQSG++ D L Sbjct: 299 -ACGTSYYSGLTAKYWIESVAKIPVNVEIASEYRYRDSVPH-PNTLVVTISQSGETADTL 356 Query: 129 AAVKAAKAAGA-HAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLI 187 AA+K A++ G H + + NV S + AG E+ VA+TK++ L A+ L Sbjct: 357 AALKHARSLGMEHTLTICNVGHSAMVRECQLAYITRAGVEVGVASTKAFTTQLAALFLLT 416 Query: 188 AAWT---------EDAELTAALQDLPTALAAAWTLDWSLAV--ERLKTASNLYVLGRGVG 236 A E+ E A++ LP A++A L+ + E N LGRG+ Sbjct: 417 LALAQVNGRLTEAEEVEHLKAMRHLPVAISAVLALEPQIIAWAEDFARKENALFLGRGMH 476 Query: 237 FGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAG 296 + +ALE ALK KE +HAEA+ A E+ HGP+ALV + P + A ND + Sbjct: 477 YPIALEGALKLKEISYIHAEAYPAGELKHGPLALVTEEMPVVTVAPNDALIEKLKSNMQE 536 Query: 297 LRARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDP 350 +RARG + + G+ + + +L PIL + S +A +VARG D Sbjct: 537 VRARGGQLYVFADVDSRITSGEGVHVIRLPEHYGLLSPILHVVSLQLLAYHAAVARGTDV 596 Query: 351 DSPPHLNK 358 D P +L K Sbjct: 597 DKPRNLAK 604 Lambda K H 0.315 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: 373 Number of extensions: 14 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: 363 Length of database: 609 Length adjustment: 33 Effective length of query: 330 Effective length of database: 576 Effective search space: 190080 Effective search space used: 190080 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 (21.6 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