Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein
Query= BRENDA::P49189 (494 letters) >MicrobesOnline__882:208821 Length = 464 Score = 179 bits (454), Expect = 2e-49 Identities = 121/401 (30%), Positives = 190/401 (47%), Gaps = 15/401 (3%) Query: 72 ERCRILLEAARIIREREDEIATMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAGEH 131 ER IL A ++R + + GK ++ ++++ + + + A A + G Sbjct: 48 ERLAILERLATLMRTHAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGRE 107 Query: 132 IQL-----PGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTP 186 + + G +T REP GV + I A+N+P + ++ PA A G ++ KP+ TP Sbjct: 108 VPMGLTPASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATP 167 Query: 187 VSALLLAEIYSEAGVPPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAK 246 +S + + EAGVP ++ AAT + L P VA +SF GS G + A Sbjct: 168 LSCRNVLRLMHEAGVPEAWATMLPCAAATAEKLVADPRVAFLSFIGSSRVGWHLRSKLAP 227 Query: 247 GIKPVTLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTE 306 G LE GG +P+++ + D++ A+ L F GQVC + RVF E F E Sbjct: 228 GAT-CALEHGGAAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAE 286 Query: 307 EVVKQTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPK 366 + ++ GDP+ DT +GPLI+ + RV +V+ A+ G VLCGG Sbjct: 287 RLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGG-------AP 339 Query: 367 LKDGYYMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTR 426 L + Y P V+ + + E+FGPV+++ S E + RAND F A VF R Sbjct: 340 LSETLY-SPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFAR 398 Query: 427 DIQRAHRVVAELQAGTCFINNYNVSPVE-LPFGGYKKSGFG 466 D+ A L A +N++ V+ +PFGG +SG G Sbjct: 399 DVDVALDTARRLNATGVMVNDHTAFRVDWMPFGGRGESGMG 439 Lambda K H 0.320 0.137 0.411 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: 559 Number of extensions: 33 Number of successful extensions: 3 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: 494 Length of database: 464 Length adjustment: 34 Effective length of query: 460 Effective length of database: 430 Effective search space: 197800 Effective search space used: 197800 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: 51 (24.3 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