Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Pedo557:CA265_RS14455 (443 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 145 bits (365), Expect = 3e-39 Identities = 125/415 (30%), Positives = 192/415 (46%), Gaps = 68/415 (16%) Query: 28 YDME--KSHGAYIYDAKHNRTLLDFFTCFASVPLGYNHPKMINDEAFKKNLFLAALANPS 85 YD+E K+ G+Y++D ++ LD + A + +G+ HP D + L+ ++ S Sbjct: 11 YDIEPVKAQGSYLWD-QNGIEYLDMYGGHAVISVGHCHP----DYVARLTEQLSKISFYS 65 Query: 86 NSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGGLAVENAIKVAMDWKVQKNFAKGYTE 145 NS QQ + + G PDY F G A ENA+K+A +K Sbjct: 66 NSVQIPQQEELATKLGTLSGYPDY--KLFLCNSGAEANENALKLASFHTGRK-------- 115 Query: 146 EKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNLSHAI 205 KV+ F +AFHGRT ++ T+ P + P++ N + Sbjct: 116 ----KVVAFTKAFHGRTAGAVAATDN------------------PSIVAPVNYNEHVSFL 153 Query: 206 QTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAFLIYD 265 + Q A +++ A+IVE IQ GG +EFL ++ DE A LI D Sbjct: 154 PFNDIEALQ-----AGITEEVAAVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILD 208 Query: 266 EVQTGVGLTGKFWCHQHFSEKARPDILAFGKKM----QVCGILVGHKVDQVETNVFKVP- 320 VQ G G TGKF+ HQ PD++ K M + G+L+ + FK Sbjct: 209 SVQCGYGRTGKFFSHQF--SGIHPDMMTMAKGMGNGFPIAGVLIAPQ--------FKASF 258 Query: 321 SRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYLKDQLENLSHRFDQMTNVRGR 380 + +T+GGN + +L I++++QL +NATK+G YL ++E L D +RGR Sbjct: 259 GLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEIEELGGYKD----LRGR 314 Query: 381 GLL--CSFDFPTKEMRNTFIAKGLENNVMFLGCGEKTIRFRPALCIEQKHIDEGL 433 GL+ FDFP KE+RN + E+++ G T+R P+L I QK D+ L Sbjct: 315 GLMIGIEFDFPVKELRNKLL---FEHHIFTGVAGAYTLRLLPSLAISQKEADQFL 366 Lambda K H 0.321 0.137 0.414 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: 431 Number of extensions: 30 Number of successful extensions: 5 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: 443 Length of database: 384 Length adjustment: 31 Effective length of query: 412 Effective length of database: 353 Effective search space: 145436 Effective search space used: 145436 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 (21.9 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