Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate AZOBR_RS01360 AZOBR_RS01360 lysine 2 3-aminomutase
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__azobra:AZOBR_RS01360 Length = 344 Score = 266 bits (679), Expect = 9e-76 Identities = 133/327 (40%), Positives = 192/327 (58%), Gaps = 1/327 (0%) Query: 40 LTKEEEEGVAQCVKSLRMAITPYYLSLIDPNDPNDPVRKQAIPTALELNKAAADLEDPLH 99 +T E VA +A+TPY L + P DP+ Q +P+ E A + EDP+ Sbjct: 16 MTPAAGEAVAAVADRYAIALTPYLLEALADAAPGDPLYAQYVPSPEEAYTAPEEREDPIG 75 Query: 100 EDTDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRRRFAGQSDDSMPMERIDKAIDYIRN 159 + SPV G+ HRYPDRVLL C++YCR C RR G +++ E +D A+ Y+R Sbjct: 76 DVVRSPVKGIVHRYPDRVLLKPLHACAVYCRFCFRREMVGPGGEALAPEELDAALAYVRA 135 Query: 160 TPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHVEIVRIGSRTPVVLPQRITPELVNML 219 P+V +V+++GGD LL+S L +I+ L +IPHV +VR+ +R PV P R+TPELV L Sbjct: 136 RPEVWEVVVTGGDPLLLSPRRLSHIVRSLSDIPHVGVVRLHTRIPVADPARVTPELVEAL 195 Query: 220 KKYH-PVWLNTHFNHPNEITEESTRACQLLADAGVPLGNQSVLLRGVNDCVHVMKELVNK 278 K W+ H NH +E+TE + A LADAG+PL Q+VLL+G+ND ++ L Sbjct: 196 KAPDLATWMAIHVNHADELTEPARGAIARLADAGIPLLGQTVLLKGINDDAAALEALFRG 255 Query: 279 LVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEIIEGLRGHTSGYCVPTFVVDAPGGGGKT 338 LV+ R++PYY++ DL+ G HFR +++G +++GLRG SG C PT+V+D PGG GK Sbjct: 256 LVRNRIKPYYLHHPDLAAGTSHFRPTLAEGQALVKGLRGRVSGLCQPTYVLDIPGGHGKA 315 Query: 339 PVMPNYVISQSHDKVILRNFEGVITTY 365 P P +V + +F G Y Sbjct: 316 PAAPGWVRPDGEGGYLAEDFTGATHRY 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: 424 Number of extensions: 17 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: 344 Length adjustment: 30 Effective length of query: 386 Effective length of database: 314 Effective search space: 121204 Effective search space used: 121204 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