Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate WP_109968124.1 DK846_RS06500 KamA family radical SAM protein
Query= BRENDA::G3F9W8 (439 letters) >NCBI__GCF_003173355.1:WP_109968124.1 Length = 374 Score = 194 bits (492), Expect = 5e-54 Identities = 116/304 (38%), Positives = 168/304 (55%), Gaps = 20/304 (6%) Query: 39 SMLEKVLGITFPPEEREKLQETIDKFPLAATPYYLSLIKTEDYANDPIFRQAVPVPDELR 98 S+ E L P++ K+++ +P + YYLSLI + NDPI R +P P Sbjct: 8 SVHETSLSDVLDPDQVLKMEDVERVYPFRSNEYYLSLINHNN-PNDPIKRIILPDP---- 62 Query: 99 VEECELE-----DPLAEDSDSPVPGITHRYPDRVLFLVSNVCAMYCRHCTRKRKVGDRDR 153 CEL DP E+ SP+PG+ H+YP + LVSN C CR C RKR + Sbjct: 63 ---CELANPGSLDPSGEEEYSPLPGVQHKYPQTAMLLVSNTCGGICRFCFRKRLFTGENP 119 Query: 154 IPTWEEMEVGITYIREHPEVRDVLLSGGDPLMLPDDLLDRILTQLRAIPHVEVIRIGSRT 213 P + + + Y++ ++ DVLLSGGDPLML LD+IL+ +R +P +IRIG++ Sbjct: 120 PPICDTKKA-VDYLQTQKDLTDVLLSGGDPLMLGASKLDQILSMIRELPTKPIIRIGTKI 178 Query: 214 PVVLPFRITDG--LVNVLKKH----QPIWLNTHFNHPQEITPSAEKALAKLADAGIPLGN 267 P P R+TD L +VL KH + I+L +HFNHPQEIT S++ A++ L + G L N Sbjct: 179 PAYDPHRLTDDSDLRDVLAKHTSPEEKIYLISHFNHPQEITSSSKAAISALKNTGAELTN 238 Query: 268 QSVLLAGVNDCPRIMKSLVQKLVKNRVRPYYLYQCDLSEGLSHFRTPVGKGIEIMENLIG 327 Q+ +L G+N+ P IM SL L K V PYY++QC + G H P+ + + ++ Sbjct: 239 QTPILQGINNEPDIMASLFNILSKLGVPPYYVFQCRPTSGNRHLTVPIEQAMHVIHEAQS 298 Query: 328 HTSG 331 SG Sbjct: 299 CCSG 302 Lambda K H 0.319 0.138 0.420 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: 429 Number of extensions: 25 Number of successful extensions: 4 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: 439 Length of database: 374 Length adjustment: 31 Effective length of query: 408 Effective length of database: 343 Effective search space: 139944 Effective search space used: 139944 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