Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_005457416.1 SACCYDRAFT_RS15225 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000244975.1:WP_005457416.1 Length = 489 Score = 387 bits (993), Expect = e-112 Identities = 211/485 (43%), Positives = 290/485 (59%), Gaps = 11/485 (2%) Query: 39 IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDA 98 +FI+ W A + T +NP V+ VAE D + AV AAR AF G WR A Sbjct: 4 LFIDGRWVPASAEATRDVLNPYDQSVVSTVAEAGATDAEAAVLAARKAFD-GGEWRDWTA 62 Query: 99 SHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHG 158 R RLL R+A+L++RDR +A ETLD GK V +D+D V YYA A+ G Sbjct: 63 RRRSRLLRRIAELLQRDRAEIARTETLDTGKTLVEGG-IDVDDVTSVFEYYATQAESDPG 121 Query: 159 KTIPIDGDFF-SYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLT 217 + + S EPVGVC I PWN+PLL AWK+ PALA GN +V+K +E TPLT Sbjct: 122 RLVDAGNPAVRSRVVFEPVGVCALIAPWNYPLLQMAWKVAPALAAGNTMVLKPSETTPLT 181 Query: 218 ALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSS 277 + + LI+EAG P GVVN+V G G G+ + H VD V+FTG GR I +A+ + Sbjct: 182 TVKMVELIEEAGAPAGVVNLVLGAGDPVGSTLVEHPQVDLVSFTGGLATGRAI-MASAAG 240 Query: 278 NLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVE 337 +K+V LELGGK+PNI+ +DAD + A++ A A+FF+ GQ C AG+R V++ +++ FV Sbjct: 241 TVKKVALELGGKNPNIVFADADFEAAIDYALIAVFFHAGQVCSAGTRLVVEDSLHERFVA 300 Query: 338 RSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD---- 393 RA+ +GN D TE GP V E K+ Y++ G +EGA+LL GG D Sbjct: 301 ELTERAERIRLGNGLDPDTESGPLVSEEHRAKVERYVSVGVEEGARLLTGGRRPDDPKLG 360 Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453 RG+F PTVF D GM + +EE FGP++ + +F +E+ V N++TYGLAAAV+T + Sbjct: 361 RGFFYLPTVFDDCHGGMRVVQEETFGPILTVERFSEVEDAVRIGNDTTYGLAAAVWTAEA 420 Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV---TV 510 +A Y+++AL+ GTVW+N + + Q+ +GGYK SG GRELG GL Y E K + T Sbjct: 421 RRAEYVARALRHGTVWINDFGPYLPQAEWGGYKRSGVGRELGHAGLAEYQEAKHIYENTA 480 Query: 511 KVPQK 515 PQ+ Sbjct: 481 PEPQR 485 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: 627 Number of extensions: 27 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: 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