Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate Echvi_4314 Echvi_4314 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase
Query= curated2:Q8Y8E7 (234 letters) >FitnessBrowser__Cola:Echvi_4314 Length = 257 Score = 135 bits (339), Expect = 1e-36 Identities = 81/240 (33%), Positives = 126/240 (52%), Gaps = 10/240 (4%) Query: 4 ITTENKLAGSKKALE----IIEKGITSGEVNTLGLATGSTPETLYAELVKSDVDTKNVTT 59 + ++ KLAG+ E I+ EV + A S L + + + V Sbjct: 10 VFSDRKLAGTAAGKEVEQCIVNLQAAQEEVRIVFAAAPSQTGMLSYLAQSTQIKWERVIA 69 Query: 60 TNLDEYVGLAASDPNSYHYYMNDLLFSKKAFKESFLPNGEATDAEAECARYEEILSEHPI 119 ++DEY+GL A P + Y+ +LFSK FK+ L D + E +RY +++E PI Sbjct: 70 FHMDEYIGLRAGAPELFASYLEQMLFSKLPFKKVNLIRTHG-DIDGELSRYGRLIAEAPI 128 Query: 120 DIQVLGIGTNGHIGFNEPGTSF--DSITHKVVLTDST---REANKRFFEREEDVPTHAYS 174 D+ LGIG NGHI FN+P + D + KVV D ++ N + F+ +DVPT A + Sbjct: 129 DLVCLGIGENGHIAFNDPPVADFDDPLVVKVVELDEACRIQQVNDKCFDHLDDVPTSAVT 188 Query: 175 MGIKSIMNAKKIILLAFGENKAQAIKETIKGPVDVNCPASVLQNHPDVTVILDNEAASLL 234 + I ++M AK ++ + GENK+QA+ +T+ PV CPAS+L HP+ + EA + L Sbjct: 189 LTIPALMAAKAMVCVVLGENKSQAVSDTLTKPVSTECPASILTTHPNCMFYFNKEAVAKL 248 Lambda K H 0.312 0.130 0.359 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: 150 Number of extensions: 5 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: 234 Length of database: 257 Length adjustment: 24 Effective length of query: 210 Effective length of database: 233 Effective search space: 48930 Effective search space used: 48930 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 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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