Align lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_040912508.1 ON01_RS12160 aldehyde dehydrogenase family protein
Query= BRENDA::Q58806 (463 letters) >NCBI__GCF_000224785.1:WP_040912508.1 Length = 481 Score = 370 bits (949), Expect = e-107 Identities = 193/468 (41%), Positives = 306/468 (65%), Gaps = 16/468 (3%) Query: 3 IDGKWIN--REDMDVINPYSLEVIKKIPALSREEAKEAIDTA-EKYKEVMKNLPITKRYN 59 I+G+ IN + + V NPY+ + +++I +S + + A+ A + + M+++P KR + Sbjct: 7 INGEEINTSNDSIKVKNPYNGDTVEEIALISDDAFERAVTGAFDTFHHTMQDMPAHKRSD 66 Query: 60 ILMNIAKQIKEKKEELAKILAIDAGKPIKQARVEVERSIGTFKLAAFYVKEHRDEVIP-- 117 IL A ++E+ ++ A+ + +AGKPI +R EV+R+I + A+ K EV+P Sbjct: 67 ILRKTADLMEERADDFAETIMKEAGKPISFSRGEVQRAIQVLRFASEEAKHISGEVVPMD 126 Query: 118 ----SDDRLIFTRREPVGIVGAITPFNFPLNLSAHKIAPAIATGNVIVHHPSSKAPLVCI 173 D RL + P+G+V AITPFNFPLNLS HKIAPAIA GN ++ P+ P+ Sbjct: 127 AAIDGDGRLGLVKHIPLGVVAAITPFNFPLNLSLHKIAPAIAAGNTVIFKPAENTPVSAY 186 Query: 174 ELAKIIENALKKYNVPLGVYNLLTGAGEVVGDEIVVNEKVNMISFTGSSKVGELITKKAG 233 +LAK+ A +P GV NLL G+G++ G+++V ++KV+ ISFTGS VG I + AG Sbjct: 187 KLAKLFHEA----GLPDGVLNLLMGSGDI-GEKLVTHDKVHKISFTGSLPVGRSIKESAG 241 Query: 234 FKKIALELGGVNPNIVLKDADLNKAVNALIKGSFIYAGQVCISVGMILVDESIADKFIEM 293 FKK+ LELG +PNI+ D ++N+AVN L+KG+F ++GQVCIS I V +SI D+F++ Sbjct: 242 FKKVTLELGSNSPNIIFDDGNINEAVNKLVKGAFAFSGQVCISAQRIYVQKSIYDQFLKE 301 Query: 294 FVNKAKVLNVGNPLDEKTDVGPLISVEHAEWVEKVVEKAIDEGGKLLLGGKRDKALFYPT 353 ++ + L +G+P E+TD+GP+IS E A+ ++ ++ A++ G K+ GG+RD+ + PT Sbjct: 302 YIKATEDLTIGDPASEETDIGPMISEEEAKRAKEWIDDAVENGAKVATGGERDETILKPT 361 Query: 354 IL-EVDRDNILCKTETFAPVIPIIR-TNEEEMIDIANSTEYGLHSAIFTNDINKSLKFAE 411 I+ V+ + + E FAP++ +I EE+++ +N + YGL + +FT D+N++ + A+ Sbjct: 362 IMTNVESNMKIIADEVFAPIVSVIPFDTEEDVVGYSNDSIYGLQAGVFTKDVNRAFRVAD 421 Query: 412 NLEFGGVVINDSSLFRQDNMPFGGVKKSGLGREGVKYAMEEMSNIKTI 459 LE GGV IN+ S +RQDN P+GGVK+SG+GREGVKYA++ M+ K I Sbjct: 422 QLEMGGVWINEISTYRQDNHPYGGVKQSGVGREGVKYAVDGMTETKFI 469 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: 601 Number of extensions: 29 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: 463 Length of database: 481 Length adjustment: 33 Effective length of query: 430 Effective length of database: 448 Effective search space: 192640 Effective search space used: 192640 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