Align Glutamate mutase sigma subunit; Glutamate mutase S chain; Glutamate mutase small subunit; Methylaspartate mutase; EC 5.4.99.1 (characterized)
to candidate BWI76_RS08490 BWI76_RS08490 methylaspartate mutase
Query= SwissProt::P80078 (137 letters) >FitnessBrowser__Koxy:BWI76_RS08490 Length = 149 Score = 160 bits (405), Expect = 7e-45 Identities = 76/135 (56%), Positives = 102/135 (75%) Query: 1 MEKKTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQEVFIKAAIETKADAILL 60 M+K T+V+GVIG+DCHAVGNK+LD FT F V+N+GV+ Q+ +I AAIET ADAI++ Sbjct: 1 MKKSTLVIGVIGADCHAVGNKVLDRVFTAHDFRVINLGVMVSQDEYIDAAIETGADAIVV 60 Query: 61 SSLYGQGEIDCKGLRQKCDEAGLEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPG 120 SS+YG G+IDC GLR++C E G+ ILLYVGGN+VVGK + DVE +FK+MG++RV+AP Sbjct: 61 SSIYGHGDIDCLGLRERCIERGIGDILLYVGGNLVVGKHDFADVEAKFKEMGFNRVFAPS 120 Query: 121 TPPEVGIADLKKDLN 135 E + D+N Sbjct: 121 HDLEDVCQLMANDIN 135 Lambda K H 0.318 0.141 0.418 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: 112 Number of extensions: 2 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: 137 Length of database: 149 Length adjustment: 16 Effective length of query: 121 Effective length of database: 133 Effective search space: 16093 Effective search space used: 16093 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 42 (20.8 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