Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_001592305.1:WP_068168204.1 Length = 485 Score = 362 bits (930), Expect = e-104 Identities = 202/465 (43%), Positives = 279/465 (60%), Gaps = 11/465 (2%) Query: 52 KTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADL 111 + F +VNP+TG V E ++DV++AV+AA A F L W M A+ RGR+L R AD+ Sbjct: 20 QVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFAL---WSAMSATERGRILRRAADI 76 Query: 112 IERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYT 171 + LAALE D GKP + +VD+ C+ Y+AG A G+ P+ + F+YT Sbjct: 77 LRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQQYPLK-NAFAYT 135 Query: 172 RHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFP 231 R EP+GVC I WN+P+ + WK PALA GN ++ K +E TP TA+ +A + EAG P Sbjct: 136 RKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLAEVYLEAGVP 195 Query: 232 PGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAAGSSNLKRVTLELGGKS 290 PGV N+V G G GA +A+H DV KV+ TGS G RV++ AAG+ LKRVT+ELGGKS Sbjct: 196 PGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGT--LKRVTMELGGKS 252 Query: 291 PNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGN 350 P ++ DAD++ AV A F+ QG+ C +R FVQ I F+ R R VG+ Sbjct: 253 PLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRFLARLKERTLLLRVGD 312 Query: 351 PFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGY---FIQPTVFGDVQ 407 P D TE G + E +++ YI +G+ EGA L+CGG A G F+ PT+F D + Sbjct: 313 PTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVEGLGDQFVAPTIFADCR 372 Query: 408 DGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGT 467 D M I +EEIFGPV+ +L F T E + RAN S + LAA VFT DL + + ++ ++AG Sbjct: 373 DDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTDLQRGHRVAAQIRAGI 432 Query: 468 VWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 W+N Y++ + PFGG SG G E L YT++KTV V++ Sbjct: 433 CWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVEL 477 Lambda K H 0.319 0.136 0.409 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: 575 Number of extensions: 27 Number of successful extensions: 6 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: 517 Length of database: 485 Length adjustment: 34 Effective length of query: 483 Effective length of database: 451 Effective search space: 217833 Effective search space used: 217833 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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