Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_086509897.1 BZY95_RS10630 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_002151265.1:WP_086509897.1 Length = 489 Score = 352 bits (904), Expect = e-101 Identities = 199/478 (41%), Positives = 269/478 (56%), Gaps = 8/478 (1%) Query: 39 IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDA 98 ++I+ A S +TF +NP G ++ +V + + D+D+AV +A Q W M Sbjct: 9 LYIDGRREPATSGETFDVLNPYDGSLLARVDQASQADIDRAVASAS---QGQRRWAAMTG 65 Query: 99 SHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHG 158 RGR+L R L+ LA LET + GKP + VD+ L YYAG A G Sbjct: 66 MQRGRVLQRAVALLRERNDELAELETRNTGKPISETAAVDIVTGADVLEYYAGLAPAIEG 125 Query: 159 KTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218 IP+ F YTR EP+GV I WN+P+ + WK PALA GN VV K +E TPLTA Sbjct: 126 AQIPLRESSFVYTRREPLGVIAAIGAWNYPIQIACWKAAPALAAGNAVVFKPSEVTPLTA 185 Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278 + +A + E G P GV N+V G G + +HE + KV+FTG G+ + AAG S Sbjct: 186 MKLAEIFTEVGLPDGVFNVVHG-EARVGQMLTAHEGIAKVSFTGEVGTGKKVMAAAGGST 244 Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 LK VT+ELGGKSP I+ +DAD+D A + A A F++ GQ C G+R FV+ + F E+ Sbjct: 245 LKDVTMELGGKSPLIVFADADLDRAADAAMMANFYSSGQICTNGTRVFVERSVKAAFEEK 304 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD----R 394 V R G+P D + GP V K+L YI GKQ+GA++L GG + R Sbjct: 305 IVERVARIRAGDPLDPEINFGPLVSFEHQAKVLDYIAYGKQDGARVLIGGEPLDEGDFAR 364 Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454 G + TVF D D M I +EEIFGPVM IL F EE++ RAN++ YGLAA VFT+ L Sbjct: 365 GAWAPATVFTDCSDEMRIVREEIFGPVMSILVFDDEEELIRRANDTHYGLAAGVFTESLA 424 Query: 455 KANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 +A+ ++AG W+N + A+ P GGYK SG GRE G L YT+ K+V V++ Sbjct: 425 RAHRTIHRMEAGICWINTWGESPAEMPVGGYKQSGVGRENGIETLAHYTQTKSVQVEM 482 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: 600 Number of extensions: 28 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: 517 Length of database: 489 Length adjustment: 34 Effective length of query: 483 Effective length of database: 455 Effective search space: 219765 Effective search space used: 219765 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 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