Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate BWI76_RS02410 BWI76_RS02410 EF-P beta-lysylation protein EpmB
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__Koxy:BWI76_RS02410 Length = 342 Score = 184 bits (467), Expect = 3e-51 Identities = 109/324 (33%), Positives = 172/324 (53%), Gaps = 4/324 (1%) Query: 19 DWRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSL-RMAITPYYLSLIDPNDPNDPVR 77 DW Q+ + + + +EL + + + + + L + + +++ ++P +PNDP+ Sbjct: 14 DWLTQLADVVTSPDELLHLLNVDADANLLAGRDARRLFALRVPRAFIARMEPGNPNDPLL 73 Query: 78 KQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRRRF 137 +Q + + E A DPL E+ S VPGL H+Y +R LLL+ C++ CR+C RR F Sbjct: 74 RQVLTSREEFVNAPGFTTDPL-EEQHSVVPGLLHKYSNRALLLVKGGCAVNCRYCFRRHF 132 Query: 138 AGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHVEIV 197 +++ A++YI + P++ +++ SGGD L+ D L++++ +L IPH++ + Sbjct: 133 P-YAENQGNKRNWQMAMEYIASHPELDEIIFSGGDPLMAKDPELDWLLTQLEAIPHIKRL 191 Query: 198 RIGSRTPVVLPQRITPELVNMLKKYH-PVWLNTHFNHPNEITEESTRACQLLADAGVPLG 256 RI SR P+V+P RIT L+ + V L H NH NEI A + L AGV L Sbjct: 192 RIHSRLPIVIPARITDTLIARISASSLQVLLVNHINHANEIDAAFRTAMKSLRIAGVTLL 251 Query: 257 NQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEIIEGLR 316 NQSVLLRGVND + +L N L V PYY++ D G HF + +I+ L Sbjct: 252 NQSVLLRGVNDDARTLADLSNALFDAGVMPYYLHVLDRVQGAAHFMVSDEEARKIMRELL 311 Query: 317 GHTSGYCVPTFVVDAPGGGGKTPV 340 SGY VP + G KTP+ Sbjct: 312 TMVSGYLVPKLAREIGGEPSKTPL 335 Lambda K H 0.320 0.138 0.422 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: 388 Number of extensions: 17 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: 416 Length of database: 342 Length adjustment: 30 Effective length of query: 386 Effective length of database: 312 Effective search space: 120432 Effective search space used: 120432 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 (21.8 bits) S2: 50 (23.9 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