Align Glutamate mutase epsilon subunit; Glutamate mutase E chain; Glutamate mutase large subunit; Methylaspartate mutase; EC 5.4.99.1 (characterized)
to candidate BWI76_RS08480 BWI76_RS08480 methylaspartate mutase subunit E
Query= SwissProt::Q05509 (485 letters) >FitnessBrowser__Koxy:BWI76_RS08480 Length = 481 Score = 583 bits (1503), Expect = e-171 Identities = 283/483 (58%), Positives = 369/483 (76%), Gaps = 3/483 (0%) Query: 1 MELKNKKWTDEEFFKQREEVLKQWPTGKEVD-LQEAVDYLKKVPTEKNFADKLVRAKEAG 59 MEL+NKK T +EF +R +VL+ W TGK+V+ ++ V Y + +P +K F+ L++A + G Sbjct: 1 MELRNKKLTHDEFMTERHQVLQTWHTGKDVEHFEDGVKYQQTIPEKKRFSHALLKADQEG 60 Query: 60 ITLAQPRAGVALLDEHINLLRYLQDEGGADLLPSTIDAYTRQNRYEECEIGIKESEKAGR 119 TL+QPRAGVAL+DEHI LL+ LQ+E DLLPSTIDAYTR NRYEE +GI++S +AG Sbjct: 61 KTLSQPRAGVALMDEHIALLKTLQEE--CDLLPSTIDAYTRLNRYEEAAVGIQKSIEAGT 118 Query: 120 SLLNGFPGVNHGVKGCRKVLESVNLPLQARHGTPDSRLLAEIIHAGGWTSNEGGGISYNI 179 S LNG P VNHGV CR++ E++ P+Q RHGTPD+RLLAEI A G+TS EGGGISYNI Sbjct: 119 SKLNGLPVVNHGVAECRRMTEALEKPVQVRHGTPDARLLAEISMASGFTSYEGGGISYNI 178 Query: 180 PYAKSVPIDKCLKDWQYCDRLVGFYEEQGVHINREPFGPLTGTLVPPSMSNAVGITEALL 239 PYAK V ++K ++DWQYCDRL+G YEE G+ INREPFGPLTGTL+PP MS+AV I E LL Sbjct: 179 PYAKRVTLEKSIRDWQYCDRLMGLYEEHGIRINREPFGPLTGTLIPPFMSHAVAIIEGLL 238 Query: 240 AAEQGVKNITVGYGECGNMLQDIAALRCLEEQTNEYLKAYGYNDVFVTTVFHQWMGGFPQ 299 A EQGVK+ITVGYG+ G++ QDIAA+R L E ++EY YG++D ++TVFHQWMGGFP+ Sbjct: 239 ALEQGVKSITVGYGQVGSLTQDIAAIRSLRELSHEYFGNYGFDDYELSTVFHQWMGGFPE 298 Query: 300 DESKAFGVIVTATTIASLAGATKVIVKTPHEAIGIPTKEANASGIKATKMALNMLEGQRM 359 DESKAF +I +A ++GATKVI K+PHEA GIPT ANA G+KA++ LNM+ Q+ Sbjct: 299 DESKAFAIISWGAAVAGMSGATKVITKSPHEAFGIPTAAANAQGLKASRQMLNMVSDQKF 358 Query: 360 PMSKELETEMAIIKAETKCILDKMFELGKGDLAVGTVKAFETGVMDIPFGPSKYNAGKMM 419 P ++ E+ +IK+E + +L K+FELG GD+A GTV AFE GV+D+PF P+ NAGK++ Sbjct: 359 PPCAAVDQEVELIKSEVRAVLKKVFELGNGDIARGTVLAFEAGVLDVPFAPASCNAGKIL 418 Query: 420 PVRDNLGCVRYLEFGNVPFTEELKNYNRERLAERAKFEGREVSFQMVIDDIFAVGKGRLI 479 PVRDN G +R LE G VP +++ + + +AERA+FEGR+ SFQMV+DDI AV +LI Sbjct: 419 PVRDNSGAIRVLEAGAVPLPKDILALHHDYVAERAQFEGRKPSFQMVVDDINAVSHSKLI 478 Query: 480 GRP 482 GRP Sbjct: 479 GRP 481 Lambda K H 0.317 0.136 0.399 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: 620 Number of extensions: 18 Number of successful extensions: 4 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: 485 Length of database: 481 Length adjustment: 34 Effective length of query: 451 Effective length of database: 447 Effective search space: 201597 Effective search space used: 201597 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: 52 (24.6 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