Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011938485.1 GURA_RS08035 aldehyde dehydrogenase
Query= BRENDA::Q58806 (463 letters) >NCBI__GCF_000016745.1:WP_011938485.1 Length = 475 Score = 364 bits (935), Expect = e-105 Identities = 202/472 (42%), Positives = 296/472 (62%), Gaps = 14/472 (2%) Query: 1 MFIDGKWI--NREDMDVINPYSLEVIKKIPALSREEAKEAIDTAEKYKEVMKNLPITKRY 58 M I G+W +R ++VINPY +I +P + E+ + AI +A K + + +P KR Sbjct: 7 MLIGGEWSGDDRTGIEVINPYDDSLIGIVPEATAEDVEAAIVSARKGFDEISAMPAYKRS 66 Query: 59 NILMNIAKQIKEKKEELAKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIPS 118 IL ++ I KEE+A I+A +AGK K A E ERS TFK AA + E++P Sbjct: 67 EILERASEFIMRDKEEIAGIIAREAGKSWKYALAEAERSAETFKFAAIEARASHGEIVPM 126 Query: 119 D------DRLIFTRREPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVC 172 D R F R P+GI+GAITPFNFPLNL AHK+APAIATGN +V P++K PL Sbjct: 127 DASPVSAGRFGFYLRNPIGIIGAITPFNFPLNLVAHKLAPAIATGNAVVLKPATKTPLTS 186 Query: 173 IELAKIIENALKKYNVPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVGELITKKA 232 ++LA+++ A +P G N++ G+G VG+ +V +E++ MI+FTGS VG I ++ Sbjct: 187 LKLAELLMEA----GLPAGALNVIIGSGATVGNRLVEDERLAMITFTGSPPVGRGIKSRS 242 Query: 233 GFKKIALELGGVNPNIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIE 292 G K++ LELG +P I+ +D D++KAV+ + GSF +GQVCISV I V +S ++FI Sbjct: 243 GLKRVTLELGSNSPTIIEEDGDVDKAVSRCVIGSFANSGQVCISVQRIFVHQSRYEEFIA 302 Query: 293 MFVNKAKVLNVGNPLDEKTDVGPLISVEHAEWVEKVVEKAIDEGGKLLLGGKRDKALFYP 352 FV + L VG+P D+ D+GP+IS + E +E+A G + +GG P Sbjct: 303 KFVEATRSLKVGDPFDKTCDIGPMISRKELERAVSWLEEAKKLGAVIAVGGNVVGNCLEP 362 Query: 353 TIL-EVDRDNILCKTETFAPVIPIIRTNE-EEMIDIANSTEYGLHSAIFTNDINKSLKFA 410 T+L V RD + +E FAP++ ++ +E +++A+ + YGL + I+T+DINK+ K Sbjct: 363 TVLTSVTRDMQVMCSEVFAPIVSVLPYKTFDEALEMADDSIYGLQAGIYTSDINKAFKAV 422 Query: 411 ENLEFGGVVINDSSLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTIIIS 462 + L+ GGV+IND FR D+MP+GG K+SGLGREGV+YAMEEM+NIK + I+ Sbjct: 423 KRLDVGGVIINDVPTFRVDHMPYGGNKESGLGREGVRYAMEEMTNIKMVCIN 474 Lambda K H 0.317 0.137 0.381 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: 602 Number of extensions: 34 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: 463 Length of database: 475 Length adjustment: 33 Effective length of query: 430 Effective length of database: 442 Effective search space: 190060 Effective search space used: 190060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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