Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_110804852.1 C8J30_RS06230 lysine-2,3-aminomutase-like protein
Query= SwissProt::Q8RHX4 (425 letters) >NCBI__GCF_003217355.1:WP_110804852.1 Length = 350 Score = 259 bits (661), Expect = 1e-73 Identities = 139/351 (39%), Positives = 206/351 (58%), Gaps = 7/351 (1%) Query: 23 TWQVKNRLESVEDLKKYVDLSEEETEGVVRTLETLRMAITPYYFSLIDLNSDRCPIRKQA 82 T VK L EDL ++ + + + + R+ +TP + I D P+ Q Sbjct: 2 TAPVKTALTCPEDLLAEGLIAPADMPALEQVAQDFRIRVTPAMRAAITAPQD--PVAAQF 59 Query: 83 IPTIQEIHQSDADLLDPLHEDEDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRRRFAGS 142 +PT E+ + DP+ + SP PGLTHRYPDR +L IT C +YCR C RR G Sbjct: 60 VPTAAELITRPEERADPIGDAVHSPAPGLTHRYPDRAILHITKTCDVYCRFCFRRETVGE 119 Query: 143 SDDAMPMDRIDKAIEYIAKTPQVRDVLLSGGDALLVSDKKLESIIQKLRAIPHVEIIRIG 202 + +P + +A+ YIA T +R+++L+GGD L +S ++LE ++ +L AIPH+ +R+ Sbjct: 120 TGP-LPEADLAQALAYIAATRGLREIILTGGDPLTLSPRRLEDVLTRLSAIPHITTLRVH 178 Query: 203 SRTPVVLPQRITPELCNMLKKYHP-IWLNTHFNHPQEVTPEAKKACEMLADAGVPLGNQT 261 SR PVV P+RITP L ++L+ P +W+ H NH QE+T A+ A L +AGVPL +Q+ Sbjct: 179 SRVPVVAPERITPALVDLLRGQRPAVWVVVHTNHAQELTAPARAALARLVEAGVPLLSQS 238 Query: 262 VLLRGINDSVPVMKRLVHDLVMMRVRPYYIYQCDLSMGLEHFRTPVSKGIEIIEGLRGHT 321 VLLRG+NDS + L L RV+PYY++ CDL+ G FRT ++ G ++ GLRGH Sbjct: 239 VLLRGVNDSHQALVDLFRALQDCRVKPYYLHHCDLAPGTSQFRTTIAAGRALVAGLRGHL 298 Query: 322 SGYAVPTFVVDAPGGGGKTPVMPQYVISQSPHRVVLR--NFEGVITTYTEP 370 SG A+PT+V+D PGG GK P+ + S P R +++G + Y +P Sbjct: 299 SGAAIPTYVLDIPGGFGKVPITADH-FSPGPRPGTWRVTDWQGGLHDYADP 348 Lambda K H 0.319 0.137 0.411 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: 432 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: 425 Length of database: 350 Length adjustment: 30 Effective length of query: 395 Effective length of database: 320 Effective search space: 126400 Effective search space used: 126400 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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