Align lysine 2,3-aminomutase (EC 5.4.3.2) (characterized)
to candidate CCNA_00753 CCNA_00753 lysine 2,3-aminomutase
Query= BRENDA::G3F9W8 (439 letters) >FitnessBrowser__Caulo:CCNA_00753 Length = 345 Score = 247 bits (630), Expect = 5e-70 Identities = 131/308 (42%), Positives = 188/308 (61%), Gaps = 3/308 (0%) Query: 50 PPEEREKLQETIDKFPLAATPYYLSLIKTEDYANDPIFRQAVPVPDELRVEECELEDPLA 109 P E L+ ++ +A TP LI D +DPI RQ VP P+EL E DP+ Sbjct: 20 PSERLPALEAVAARYAVAITPAMAELIDP-DRDDDPIARQFVPSPEELVSSPGEDGDPIG 78 Query: 110 EDSDSPVPGITHRYPDRVLFLVSNVCAMYCRHCTRKRKVGDRDRIP-TWEEMEVGITYIR 168 + + SPV GI HRYPDRVL ++ CA+YCR C R+ VG T +++ YI Sbjct: 79 DAAHSPVEGIVHRYPDRVLLKPTHTCAVYCRFCFRREMVGPEGLSNLTPAQLDAAFAYIA 138 Query: 169 EHPEVRDVLLSGGDPLMLPDDLLDRILTQLRAIPHVEVIRIGSRTPVVLPFRITDGLVNV 228 + P++ +V+++GGDPL+L L ++ +L AI HV+++R +R P V P +T LV Sbjct: 139 QRPQIWEVIVTGGDPLVLSPRRLADLMDRLEAIDHVKIVRFHTRVPAVDPGAVTPELVAA 198 Query: 229 LKKH-QPIWLNTHFNHPQEITPSAEKALAKLADAGIPLGNQSVLLAGVNDCPRIMKSLVQ 287 LK+ + +++ H NH +E+TP+A A A++ DAG+P+ +Q+VLL GVND P + L++ Sbjct: 199 LKRSSKTVYVALHANHARELTPAARAACAQIVDAGVPMVSQTVLLRGVNDNPETLVELMR 258 Query: 288 KLVKNRVRPYYLYQCDLSEGLSHFRTPVGKGIEIMENLIGHTSGFAVPTYVIDAPGGGGK 347 V+ R+RPYYL+ DL+ G +H RT V +G IM L G SG A PTYV+D PGG GK Sbjct: 259 AFVETRIRPYYLHHGDLAPGTAHLRTTVAEGQAIMRALRGTLSGLAQPTYVLDIPGGHGK 318 Query: 348 IPVMPTYL 355 +PV P YL Sbjct: 319 VPVGPNYL 326 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: 416 Number of extensions: 24 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: 439 Length of database: 345 Length adjustment: 30 Effective length of query: 409 Effective length of database: 315 Effective search space: 128835 Effective search space used: 128835 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 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