Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_040661330.1 ON16_RS08890 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_000307265.1:WP_040661330.1 Length = 612 Score = 110 bits (276), Expect = 8e-29 Identities = 102/337 (30%), Positives = 169/337 (50%), Gaps = 48/337 (14%) Query: 54 LAQRLRANPPRVVVTCARGSSDHAATFARY----LIETKAGVLTSSAGPSVSSVYDASPN 109 L Q N R+ + A GSS H ++Y L+ V+ +S + D Sbjct: 287 LTQEYVKNISRIFII-ACGSSYHVGMVSKYNWEKLLRRPVEVVLASEFRYCDPLVD---- 341 Query: 110 LEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELS 169 E +L + ISQSG++ D +AA++ AK G +A+VNVV S +A AD+V+ AGPE++ Sbjct: 342 -EHSLVVVISQSGETLDTMAAMREAKRRGGRTLAIVNVVGSSIARDADDVLYTWAGPEIA 400 Query: 170 VAATKSYIAALVAVTQLIAAWTED-------AELTAA---LQDLPTALAAAW--TLDWSL 217 VA TK+Y L A+ ++ + D + TAA +Q LP ++A T D Sbjct: 401 VATTKAYSTQL-ALMDMVGLYLGDLLGTVCKEDYTAAVEGIQRLPEQMSAFLKDTEDIKY 459 Query: 218 AVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPA 277 R ++++ +GR + + + +E +LK KE +H+EA+++ E+ HG ++L++ G Sbjct: 460 FASRYFNHNSIFFIGRNLDYAMGMEGSLKLKEISYIHSEAYASGELKHGTISLIEPG--T 517 Query: 278 LVFAQN------DESRASVDEMAAGLRARGASVLIAGGG---------GDAPDALP-TLA 321 LV A D++ ++V E ++ARGA V+ DA A+P T+A Sbjct: 518 LVVALGSYTPLFDKAMSNVVE----VKARGAEVMALATNSQKAKMEKTADAVIAVPDTIA 573 Query: 322 SHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNK 358 +L+P L + A +++ RG D D P +L K Sbjct: 574 ---MLQPSLGVVPLQLFAYYVALQRGCDIDKPRNLAK 607 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: 321 Number of extensions: 13 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: 363 Length of database: 612 Length adjustment: 33 Effective length of query: 330 Effective length of database: 579 Effective search space: 191070 Effective search space used: 191070 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