Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 224 bits (571), Expect = 5e-63 Identities = 146/464 (31%), Positives = 242/464 (52%), Gaps = 20/464 (4%) Query: 30 KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAARIIRERED 89 K P G V + F + A+ A A K S+ + +RC LL+ A + + ++ Sbjct: 19 KRVNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKE 78 Query: 90 EIATMECINNGKSIFEARLDIDISWQCLEYYAGLAASMAGEHIQLPGGSFG-----YTRR 144 +IA GK I +R++++ + + A +M GE + + G + R Sbjct: 79 DIAKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSR 138 Query: 145 EPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIY--SEAGVP 202 P GV V I +N+P + + K APAL GNA++ KP+P P++A A+++ SE + Sbjct: 139 VPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIK 198 Query: 203 PGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPLI 262 L +VV G A G L +SFTGSV G +I+ SA GIK V+LELGG + Sbjct: 199 DAL-SVVYGDADVGGTLVTSEIPRVISFTGSVGVG-EIITKSA-GIKKVSLELGGNAATF 255 Query: 263 IFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPLL 322 I +++ A + + F+ GQVC + R++V K+I +F ++ + T+++ +G P Sbjct: 256 IDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYE 315 Query: 323 EDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNCR 382 EDT MGPL+N +R + +V+ A ++GA + +P++ +G PCV+ + + Sbjct: 316 EDTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL--------EPRV-EGRVFYPCVMADVK 366 Query: 383 DDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAGT 442 +DM V +E+F P++S++ E L N++ +GL +FT D+ R + EL AG Sbjct: 367 EDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGG 426 Query: 443 CFINNYNVSPVEL-PFGGYKKSGFGRENGRVTIEYYSQLKTVCV 485 IN+ ++ P+GG K SG GRE R IE S++K+V + Sbjct: 427 IVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 510 Number of extensions: 21 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: 494 Length of database: 471 Length adjustment: 34 Effective length of query: 460 Effective length of database: 437 Effective search space: 201020 Effective search space used: 201020 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