Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092483144.1 BM299_RS08870 glutamate 2,3-aminomutase
Query= SwissProt::Q9XBQ8 (416 letters) >NCBI__GCF_900115975.1:WP_092483144.1 Length = 413 Score = 388 bits (996), Expect = e-112 Identities = 184/361 (50%), Positives = 259/361 (71%), Gaps = 3/361 (0%) Query: 4 RRYEL--FKDVSDADWNDWRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITP 61 R+ EL F ++ +W DW WQ+RNRI V L+K LT+EE E + + R A++P Sbjct: 46 RKKELLQFFGATEENWQDWHWQMRNRISDVGMLRKLWSLTEEEAEQIESVSEKFRWAVSP 105 Query: 62 YYLSLIDPNDPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLI 121 YYLSL++P +P PVR Q IP+ EL L DP+ E+ SP P +T RY DR+++ + Sbjct: 106 YYLSLMEPGNPGCPVRMQGIPSIRELQDNWGKL-DPMAEEYTSPAPRITRRYADRLIINV 164 Query: 122 TDMCSMYCRHCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETL 181 T+ C+M+CRHC RRR G+ D P+E I AIDYIR P+VRDVL++GGD L +SDE L Sbjct: 165 TNQCAMFCRHCQRRRSIGEVDKPAPVEEIKAAIDYIRQNPEVRDVLITGGDPLTLSDEWL 224 Query: 182 EYIIAKLREIPHVEIVRIGSRTPVVLPQRITPELVNMLKKYHPVWLNTHFNHPNEITEES 241 ++I+++L +I HVEI RIGSRTPV +PQRITPEL ML+ +HP++LNTHFNHP E+T+E+ Sbjct: 225 DWILSELDKIEHVEIKRIGSRTPVTMPQRITPELCAMLESHHPLYLNTHFNHPREVTQEA 284 Query: 242 TRACQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHF 301 RA ++LA AG+ LGNQ+VLL+G+N+ HVMK+L ++L+KI VRPYYI+ G HF Sbjct: 285 LRATRMLAKAGISLGNQAVLLKGINNDPHVMKKLNHELLKIHVRPYYIFHAKPVKGTTHF 344 Query: 302 RTPVSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKTPVMPNYVISQSHDKVILRNFEGV 361 T V +G+EI+E LRG+TSG +P ++++APGG GKTP++P Y+++ D V++R +EG Sbjct: 345 VTTVQEGLEIMENLRGYTSGLAIPWYIINAPGGAGKTPLLPQYLLTMGKDYVMIRTWEGK 404 Query: 362 I 362 + Sbjct: 405 V 405 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: 498 Number of extensions: 14 Number of successful extensions: 2 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: 413 Length adjustment: 31 Effective length of query: 385 Effective length of database: 382 Effective search space: 147070 Effective search space used: 147070 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 Apr 09 2024. 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