Align glucosamine-6-phosphate deaminase subunit (EC 3.5.99.6) (characterized)
to candidate WP_054654195.1 CES79_RS05010 glucosamine-6-phosphate deaminase
Query= metacyc::MONOMER-13104 (235 letters) >NCBI__GCF_002217945.1:WP_054654195.1 Length = 237 Score = 257 bits (657), Expect = 1e-73 Identities = 127/233 (54%), Positives = 165/233 (70%) Query: 1 MKIIQVENQVEGGKVALELLKEKLAQGAKTLGLATGSSPEEFYKQIVESDLDFSEMTSVN 60 M +I V+N+ EGGK E+ + GA+ GLATGS+P Y+++ +SDLDFS+MTSVN Sbjct: 1 MNVIIVKNRAEGGKKGFEVFENAYRNGAQVFGLATGSTPVTTYEELTQSDLDFSQMTSVN 60 Query: 61 LDEYVGLQEEDPQSYRYFMNQHLFNQKPFKASFLPNGAAKDLEAEVARYNQLLTEHPADL 120 LDEYVGL + PQSY YFM QHLF+QKPF S++P+G D AE+ RY+Q++ ++P DL Sbjct: 61 LDEYVGLAPDHPQSYHYFMQQHLFDQKPFAHSYVPDGLNSDAAAEMKRYDQIIADNPIDL 120 Query: 121 QILGIGTNGHIGFNEPGTSFDSQTHLVDLTPSTIQSNARFFDKMEDVPTQAISMGIGNIL 180 QILG+G NGHIGFNEPGT TH V LT STI++N+RFFD ++VP A SMGI +IL Sbjct: 121 QILGLGQNGHIGFNEPGTDPALGTHKVALTESTIKANSRFFDNEDEVPRYAYSMGIASIL 180 Query: 181 NAKSIILFAYGSAKAKAIAGTVEGEVTEELPGSALQKHPDVVIIADKEALSLL 233 +K I+L AYG KA A+ +EG VT ++P S LQ+H V II D+ A S L Sbjct: 181 KSKHILLEAYGPEKAAAVKAMIEGPVTTDVPASFLQRHDQVTIIIDEAAASQL 233 Lambda K H 0.313 0.132 0.362 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: 184 Number of extensions: 7 Number of successful extensions: 1 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: 235 Length of database: 237 Length adjustment: 23 Effective length of query: 212 Effective length of database: 214 Effective search space: 45368 Effective search space used: 45368 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 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