Align L-lysine 2,3-aminomutase; LAM; KAM; EC 5.4.3.2 (characterized)
to candidate WP_092481457.1 BM299_RS00240 KamA family radical SAM protein
Query= SwissProt::Q9XBQ8 (416 letters) >NCBI__GCF_900115975.1:WP_092481457.1 Length = 357 Score = 286 bits (731), Expect = 9e-82 Identities = 144/353 (40%), Positives = 233/353 (66%), Gaps = 15/353 (4%) Query: 20 WRWQVRNRIETVEELKKYIPLTKEEEEGVAQCVKSLRMAITPYYLSLIDPNDPNDPVRKQ 79 W++Q++N + T+++L+K+I +T+EE E +A + + TPY+ L+D +DPN P+RKQ Sbjct: 4 WQYQMQNFVNTIDKLEKFINITQEEREAIAST--NTKWGTTPYFAGLMDRDDPNCPIRKQ 61 Query: 80 AIPTALE-LNKAAAD---LEDPLHEDTDSPVPGLTHRYPDRVLLLITDMCSMYCRHCTRR 135 IP+ E +N+ + + + + + +Y DR+ + ++C+ YCRHC R+ Sbjct: 62 VIPSPREKVNRYGIENYLIYKENRSNEEKRPDTIARQYHDRIAFTVMNICANYCRHCFRK 121 Query: 136 RFAGQSDDSMPME-RIDKAIDYIRNTPQVRDVLLSGGDALLVSDETLEYIIAKLREIPHV 194 D+S+ +D+ + +IR ++RDVL++GGD LL++++ LEYII+KLR+IPH+ Sbjct: 122 ELV--VDESLHFNFNVDEGLAWIREHNEIRDVLITGGDPLLLANDKLEYIISKLRDIPHI 179 Query: 195 EIVRIGSRTPVVLPQRITPELVNMLKKYH--PVWLNTHFNHPNEITEESTRACQLLADAG 252 E++R GSR P+VLP RIT L+ +L +H P+WLNT NH EITE++ A L AG Sbjct: 180 EMIRFGSRVPIVLPHRITDGLLKVLGGFHKVPIWLNTQCNHAKEITEQTAEAVYKLMTAG 239 Query: 253 VPLGNQSVLLRGVNDCVHVMKELVNKLVKIRVRPYYIYQCDLSLGLEHFRTPVSKGIEII 312 V +GNQ+VLL+G+ND KEL KL+ +R+RPYY++ C+ + G++HFRTPV KG E+I Sbjct: 240 VNVGNQAVLLKGINDDKKSFKELHQKLLTVRIRPYYVFYCEPAPGIDHFRTPVEKGAELI 299 Query: 313 -EGLRGHTSGYCVPTFVVDAPGGGGKTPVMPN-YVISQSHDKVILRNFEGVIT 363 + LRGHT+G P +V+ GK P+MP+ Y++ ++ ++ L+N++G IT Sbjct: 300 RDCLRGHTTGLAQPMYVMAT--NIGKIPLMPDYYIMDKNEEEYTLKNYKGQIT 350 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: 441 Number of extensions: 26 Number of successful extensions: 8 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: 357 Length adjustment: 30 Effective length of query: 386 Effective length of database: 327 Effective search space: 126222 Effective search space used: 126222 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 Apr 09 2024. 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