Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate GFF2570 HP15_2514 lysine 2,3-aminomutase YodO family protein
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__Marino:GFF2570 Length = 346 Score = 186 bits (471), Expect = 1e-51 Identities = 109/331 (32%), Positives = 169/331 (51%), Gaps = 3/331 (0%) Query: 12 VSDADWNDWRWQVRNRIETVEELKKYIPLTKEEE-EGVAQCVKSLRMAITPYYLSLIDPN 70 +SD + W+ + + + +EL + + L +E G Q + ++ + +L+ ++ Sbjct: 13 LSDHEQRSWQQLLSGAVTSPKELLRRLELPEEPWLAGAEQGHRLFQIRVPEPFLNRMEKG 72 Query: 71 DPNDPVRKQAIPTALELNKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCR 130 +P DP+ +Q +P A E A + DPL E GL +Y R LL++T C++ CR Sbjct: 73 NPADPLLRQVLPLADEAGHAPGFVSDPLEESGAIATTGLIRKYRSRALLMVTGQCAINCR 132 Query: 131 HCTRRRFAGQSDDSMPMERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLRE 190 +C RR F P +R + ID + +P++ +V+ SGGD L V+D L + + Sbjct: 133 YCFRRHFPYDEQRLSPHDR-QRVIDVLGASPEINEVIFSGGDPLAVNDRLLSQWASAISG 191 Query: 191 IPHVEIVRIGSRTPVVLPQRITPELVNMLKKYH-PVWLNTHFNHPNEITEESTRACQLLA 249 IPH+ +R+ +R PVV+PQR+ EL+ L V + H NHP EI + RA L Sbjct: 192 IPHIRRLRLHTRLPVVIPQRVCDELLKWLSTTPLQVVIVLHINHPAEIDGPTRRALGYLR 251 Query: 250 DAGVPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGI 309 AG L NQSV+LRGVND V++EL L V PYY++ D G HF + Sbjct: 252 AAGATLLNQSVILRGVNDRTAVLEELSETLFDAGVLPYYLHAFDPVTGAHHFDVSDDEAR 311 Query: 310 EIIEGLRGHTSGYCVPTFVVDAPGGGGKTPV 340 ++ L G+ VP V + PG KTP+ Sbjct: 312 NLVRELLARLPGFLVPKLVREEPGKESKTPI 342 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: 422 Number of extensions: 22 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: 416 Length of database: 346 Length adjustment: 30 Effective length of query: 386 Effective length of database: 316 Effective search space: 121976 Effective search space used: 121976 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