Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate Pf6N2E2_2163 Lysine 2,3-aminomutase (EC 5.4.3.2)
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2163 Length = 465 Score = 226 bits (576), Expect = 1e-63 Identities = 137/362 (37%), Positives = 202/362 (55%), Gaps = 27/362 (7%) Query: 4 RRYELFKDVSDADWNDWRWQVRNRIETVEELKKYIP------LTKEEEEGVAQCVKSLRM 57 R + +KD+ + + WQ +N I +V L I ++ EEG S+R+ Sbjct: 45 RDLDHWKDIDVELFLNHLWQEKNAITSVGALGALIKNRISAAFLRDLEEGHQMAPMSIRL 104 Query: 58 AITPYYLSLIDPNDPN-DPVRKQAIPTALELNKAAADLE-DPLHEDTDSPVPGLTHRYPD 115 TPY LSLID ++P DP+R+Q +P A E++ ++ DP+ E DSP PGLTHRYPD Sbjct: 105 --TPYILSLIDWDNPYLDPLRRQFLPLASEISIDHPMVKLDPMGEQDDSPAPGLTHRYPD 162 Query: 116 RVLLLITDMCSMYCRHCTRRRFAGQSDDSM-------PMERIDKAIDYIRNTPQVRDVLL 168 RVL L T++C +YCR+CTR G D++ P ER + A+ YI V DV++ Sbjct: 163 RVLFLATNVCPVYCRYCTRSYAVGLDTDAVTKKKINAPGERWEPALRYIETNSSVEDVVI 222 Query: 169 SGGDALLVSDETLEYIIAKLREIPHVEIVRIGSRTPVVLPQRITPE---------LVNML 219 SGGDA + + I +L ++PHV +R ++ VLP +I + L + Sbjct: 223 SGGDAYRLKARQITEIGERLLDVPHVRRMRFATKGLAVLPMKIQSDHDWTDAISRLSDRA 282 Query: 220 KKYHP-VWLNTHFNHPNEITEESTRACQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNK 278 +K H + ++THFNHPNEIT + +A +L + GV + NQ+V+L+GVND M L Sbjct: 283 RKVHKSIAIHTHFNHPNEITAVTAKALGMLYERGVEVRNQAVILKGVNDNPQTMHRLNEC 342 Query: 279 LVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKT 338 L + VRPYY +Q D+ G+E RT + I + + RG +G+ P F+VD PGGGGK Sbjct: 343 LAYLNVRPYYCFQGDMIRGVEALRTSLCDSIALEKSTRGLIAGHNTPHFIVDLPGGGGKR 402 Query: 339 PV 340 + Sbjct: 403 DI 404 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: 531 Number of extensions: 25 Number of successful extensions: 5 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: 465 Length adjustment: 32 Effective length of query: 384 Effective length of database: 433 Effective search space: 166272 Effective search space used: 166272 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: 51 (24.3 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