Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Putida:PP_5063 Length = 490 Score = 215 bits (547), Expect = 4e-60 Identities = 145/456 (31%), Positives = 234/456 (51%), Gaps = 17/456 (3%) Query: 71 PANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALREKIQVLGS 130 PA E +A V++A+ AD E+ V+ A K+WA + A +R I+R+ D LRE+ L Sbjct: 29 PATGEVLAHVQRATEADVEKAVESAERGQKVWAAMTAMQRSRILRRAVDILRERNDELAM 88 Query: 131 LVSLEMGKILVEG-VGEVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQWNPVGLVG 189 L +L+ GK E ++ D+ +Y GL I G +P S + P+G+ Sbjct: 89 LETLDTGKSYSETRYVDIVTGADVLEYYAGLVPAIEGEQIPLRESSFVYTRR-EPLGVTV 147 Query: 190 IITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVLEDNKLPGAICS 249 I A+N+P+ + W +A A+ GN ++K + TSL ++ +A++ + LP + + Sbjct: 148 GIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLK----LAEIYTEAGLPNGVFN 203 Query: 250 -LTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSL-LELGGNNAIIAFE 307 LT G ++GT + + R+ +SFTG T GK+V + + +ELGG + +I Sbjct: 204 VLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMASASSSSLKEVTMELGGKSPLIICA 263 Query: 308 DADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQIRVGNPWDPNV 367 DADL A+ A ++GQ CT R+FI + ++ + A+IRVGNP D N Sbjct: 264 DADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEMKAAFEAKIAERVARIRVGNPEDENT 323 Query: 368 LYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMD----RPGNYVEPTIVTGLGHDASI 423 +GPL + Q + LG + + K+EG V+ GG+ + G +V PT+ T D +I Sbjct: 324 NFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERLTAGDFAKGAFVAPTVFTDCTDDMTI 383 Query: 424 AHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGIVNV 483 E F P++ + ++ EEEV N+ GL++ + T D+ R R + + GI + Sbjct: 384 VKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAGVCTNDITRAHRII--HKLEAGICWI 441 Query: 484 NI-PTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518 N S AE+ GG K +G GRE+G + QY R Sbjct: 442 NAWGESPAEM--PVGGYKQSGVGRENGVSSLAQYTR 475 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: 694 Number of extensions: 38 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: 539 Length of database: 490 Length adjustment: 35 Effective length of query: 504 Effective length of database: 455 Effective search space: 229320 Effective search space used: 229320 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 17 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