Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate SMc00355 SMc00355 hypothetical protein
Query= SwissProt::Q9XBQ8 (416 letters) >FitnessBrowser__Smeli:SMc00355 Length = 350 Score = 242 bits (618), Expect = 1e-68 Identities = 125/335 (37%), Positives = 190/335 (56%), Gaps = 2/335 (0%) Query: 28 IETVEELKKYIPLTKEEEEGVAQCVKSLRMAITPYYLSLIDPNDPNDPVRKQAIPTALEL 87 I T EL + +E+EE +++ +AI+P L+D +DPNDP+ +Q +P EL Sbjct: 7 IRTARELADAGLVGREQEEAISRVASRYAVAISPTIARLVDRDDPNDPIARQFVPDMAEL 66 Query: 88 NKAAADLEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRRRFAGQSD-DSMP 146 + DP+ + SPV G+ HRYPDRVLL +C +YCR C RR G ++ Sbjct: 67 TLMPEERADPIGDGAHSPVAGIVHRYPDRVLLKAVHVCPVYCRFCFRREMVGPEGLGTLT 126 Query: 147 MERIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHVEIVRIGSRTPVV 206 +D A+ YI P++ +V+L+GGD L++S L I+ +L EI HV++VR +R PVV Sbjct: 127 PAELDAALAYIAGRPEIWEVILTGGDPLVLSPRRLGDIMVRLAEIDHVKVVRFHTRVPVV 186 Query: 207 LPQRITPELVNMLKKY-HPVWLNTHFNHPNEITEESTRACQLLADAGVPLGNQSVLLRGV 265 P R+ L+ LK ++ H NHP E+T E+ A L DAG+ + +QSVLL+GV Sbjct: 187 EPDRVDAGLIAALKSSGKATYVALHANHPRELTAEARAAAARLIDAGIVMVSQSVLLKGV 246 Query: 266 NDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEIIEGLRGHTSGYCVP 325 ND V+ L+ V+ R++PYY++ DL+ G HFR + +G ++ LRG SG C P Sbjct: 247 NDDPDVLAALMRAFVETRIKPYYLHHPDLAPGTGHFRLSIEEGQALVASLRGRVSGLCQP 306 Query: 326 TFVVDAPGGGGKTPVMPNYVISQSHDKVILRNFEG 360 +++D PGG GK V + ++ + +F G Sbjct: 307 AYILDIPGGHGKAVVSAGAIEAEGGGCYTVTDFRG 341 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: 407 Number of extensions: 19 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: 350 Length adjustment: 30 Effective length of query: 386 Effective length of database: 320 Effective search space: 123520 Effective search space used: 123520 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