Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_178371896.1 BUB04_RS04110 aldehyde dehydrogenase family protein
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_900129305.1:WP_178371896.1 Length = 481 Score = 311 bits (798), Expect = 2e-89 Identities = 186/457 (40%), Positives = 258/457 (56%), Gaps = 11/457 (2%) Query: 33 EPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARIIREREDEIA 92 +PATG+VIA ++ V+ AV A A W+ R +LLE AR + R D+++ Sbjct: 30 DPATGQVIARVPLCNDQVVDKAVAGALRAQPSWADAPVEHRTSLLLEWARAVSSRLDQLS 89 Query: 93 TMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAGEHIQLPG--GSFGYTRREPLGVC 150 + C GK + AR +++ + Q + Y+A A + G H+ L G GS REP+GV Sbjct: 90 LLNCRETGKPLHAARAEVENAVQLIHYFAEEARRLTG-HLPLTGQPGSQTLVFREPVGVV 148 Query: 151 VGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGVPPGLFNVVQ 210 I +NYP K+ PALA G A+V KP TP++ L LA + EAG+PPG+F VV Sbjct: 149 AAITPFNYPISTLVTKATPALAVGCAVVAKPDEHTPLATLELARLAEEAGLPPGVFQVVT 208 Query: 211 G-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPLIIFSDCDM 269 G G TG+ L HP VA V+FTGS G I +++A G+K + LELGG P I+ D D Sbjct: 209 GPGPETGRALAAHPKVALVTFTGSTEVGKFIQKLAADGVKRLILELGGHCPAILCRDADW 268 Query: 270 NNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPLLEDTRMGP 329 + L F GQ C TR++V +EI D E++ +K GDP +T +GP Sbjct: 269 VRLLPSILSQAFKNSGQYCYRITRLYVAREIWDAVLEKLTSAAATLKAGDPRDPETDLGP 328 Query: 330 LINRPHL-ERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNCRDDMTCV 388 L N PH+ +RV V+ A QGA + GG P G Y P VLT+ R M + Sbjct: 329 L-NNPHIFDRVRKQVQKALSQGAALALGGP-----PPGKDSGLYFPPTVLTDLRPGMDIL 382 Query: 389 KEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAGTCFINNY 448 +EEIFGPV+ +L F E E ++ ANDT FGLAA VF D+ RA R+ +QAG+ +IN+ Sbjct: 383 REEIFGPVLLVLPFSDEQEAVDGANDTPFGLAAYVFCGDLSRALRMAHRIQAGSVWINDI 442 Query: 449 NVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCV 485 + + E PFGG K+SG GRE R +E +++LKT+ V Sbjct: 443 HQARPEAPFGGMKQSGLGREKSRFGVEAFTELKTIYV 479 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: 585 Number of extensions: 26 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: 494 Length of database: 481 Length adjustment: 34 Effective length of query: 460 Effective length of database: 447 Effective search space: 205620 Effective search space used: 205620 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 Apr 09 2024. 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