Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_003463886.1 J416_RS02285 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_000359605.1:WP_003463886.1 Length = 600 Score = 119 bits (298), Expect = 2e-31 Identities = 94/301 (31%), Positives = 146/301 (48%), Gaps = 14/301 (4%) Query: 70 ARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLA 129 A G+S HA + IE + + S S Y+ E L++ ISQSG++ D + Sbjct: 297 AAGTSYHAGLVGKQFIERLSNIPVEVHIASEFS-YNMPLLSEKPLFIFISQSGETADSRS 355 Query: 130 AVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAA 189 + K G A+ L NV S L+ AD + LHAGPE++VA+TK+Y A +AV ++A Sbjct: 356 VLVQTKELGHPALTLTNVPGSTLSREADYTLHLHAGPEIAVASTKAYTAQ-IAVLAILAV 414 Query: 190 WTEDAE----LTAALQDLPTALAAAWTL-DWSLAVERLK-----TASNLYVLGRGVGFGV 239 T A+ L++L A +L D A +R+ T N + +GRG+ + V Sbjct: 415 DTAKAKGINLSFDPLKELGIVANAMESLTDQKDAFDRIAKDLFDTTRNAFFIGRGMDYFV 474 Query: 240 ALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRA 299 LEAALK KE + AE F+ E+ HG +AL++DG P + + + S+ + A Sbjct: 475 VLEAALKLKEISYIQAEGFAGGELKHGTIALIEDGTPVIAISSQENVNLSIRGNVQEVAA 534 Query: 300 RGASVLIAGGGG--DAPDALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLN 357 RGA+ + G D H +L P++ + +A ++ R D D P +L Sbjct: 535 RGANTCVVSMKGLEQNEDRFVLPQVHELLAPLVSVIPMQLLAYYAALHRDCDVDKPRNLA 594 Query: 358 K 358 K Sbjct: 595 K 595 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: 333 Number of extensions: 13 Number of successful extensions: 2 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: 600 Length adjustment: 33 Effective length of query: 330 Effective length of database: 567 Effective search space: 187110 Effective search space used: 187110 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