Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= BRENDA::P49419 (539 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 224 bits (571), Expect = 6e-63 Identities = 142/461 (30%), Positives = 231/461 (50%), Gaps = 22/461 (4%) Query: 63 GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122 G I PA E IA V A+ A ++ + A A K WA + +RG I+R+ D +R Sbjct: 23 GTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAADMMR 82 Query: 123 EKIQVLGSLVSLEMGKILVEGVG-EVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQ 181 E+ L L + + GK E + + D +Y GL+ + G + L E Sbjct: 83 ERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHIQ-------LGED 135 Query: 182 W-----NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAK 236 W P+G+ I A+N+P + W A A+ CGN ++K + TT L ++ V A+ Sbjct: 136 WVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKV----AE 191 Query: 237 VLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLE 296 +L + LP I ++ G ++G ++ D RV +S TGS GK+V E+ +E Sbjct: 192 ILHEAGLPAGIYNVVQGLGEVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHVTME 251 Query: 297 LGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQ 356 LGG + ++ F+DADL V A+ ++GQ C+ R+F+ + I + + RL + + Sbjct: 252 LGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTERLST 311 Query: 357 IRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTG 416 VG+P D +GP+ +++ + + L +E+ + EG +V GG+ ++R G Y++PT+ Sbjct: 312 AVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQPTVFAD 371 Query: 417 LGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGP-KG 475 + D IA E F P++ V F+ EEE N + GLS+ +FT+DL R R + + Sbjct: 372 VKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQLEA 431 Query: 476 SDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQY 516 C I + N A + FGG K +G GRE+ A Y Sbjct: 432 GSCFINSYN----DAPVEAPFGGTKMSGVGRENSKAAINHY 468 Lambda K H 0.318 0.136 0.417 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: 667 Number of extensions: 33 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: 539 Length of database: 485 Length adjustment: 35 Effective length of query: 504 Effective length of database: 450 Effective search space: 226800 Effective search space used: 226800 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 (21.7 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