Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_089214888.1 CHB69_RS04915 SIS domain-containing protein
Query= reanno::Caulo:CCNA_00453 (363 letters) >NCBI__GCF_900188185.1:WP_089214888.1 Length = 348 Score = 324 bits (831), Expect = 2e-93 Identities = 178/340 (52%), Positives = 226/340 (66%), Gaps = 4/340 (1%) Query: 27 THMFREAGEAARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYLIE 86 T MF EA A Q I + + L A+PP +VVTCARGSSDHAATFA+Y E Sbjct: 10 TLMFLEAASAGDAVERQFGCAQGVIIDILRSLAADPPSMVVTCARGSSDHAATFAKYAFE 69 Query: 87 TKAGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVN 146 + G +T+SA PS+SS+Y A L G+L+LAISQSGKSPDLL AV+ A GA +ALVN Sbjct: 70 RQLGWVTASAAPSISSIYQAPLKLGGSLFLAISQSGKSPDLLEAVERASHQGARTLALVN 129 Query: 147 VVDSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAW-TEDAELTAALQDLPT 205 D+PL+ +AD +PL AGPE SVAATKSYIA+L A+ +++ + D + L LP Sbjct: 130 APDTPLSKIADWTLPLCAGPENSVAATKSYIASLAAIARIVGSLERNDGGIAPDLAALPG 189 Query: 206 ALAAAWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLH 265 L AAW LDWS + L+VLGRG G +A EAALKFKETCG+HAEAFS AEV H Sbjct: 190 LLRAAWRLDWSPMAAAFNESQGLFVLGRGPGLAIAQEAALKFKETCGIHAEAFSTAEVRH 249 Query: 266 GPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGG--GDAPDALPTLASH 323 GPMAL G P L+F Q+DES + VD + L A GA +L+AG G G A + LP + + Sbjct: 250 GPMALAATGLPMLIFRQDDESASGVDALIKELLAIGAKLLVAGSGPCGGAIN-LPVVDAP 308 Query: 324 PVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVTETI 363 L+P+L IQSFY+ ++L+++RG+DPD PP L KVTET+ Sbjct: 309 AALQPMLQIQSFYKAISSLAISRGHDPDRPPLLRKVTETV 348 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: 398 Number of extensions: 9 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: 348 Length adjustment: 29 Effective length of query: 334 Effective length of database: 319 Effective search space: 106546 Effective search space used: 106546 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: 49 (23.5 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