Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Betaine aldehyde dehydrogenase; BADH; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_054343391.1 Nant_RS19705 betaine-aldehyde dehydrogenase
Query= SwissProt::P56533 (503 letters) >NCBI__GCF_001305295.1:WP_054343391.1 Length = 484 Score = 514 bits (1325), Expect = e-150 Identities = 258/459 (56%), Positives = 330/459 (71%), Gaps = 3/459 (0%) Query: 43 PATGRVLCQMVPCGAEEVDQAVQSAQAAYLKWSKMAGIERSRVMLEAARIIRERRDNIAK 102 PATG VL ++ +VD+AV++AQA +L WS M+G ER R+++ A I+RER D +A Sbjct: 25 PATGEVLAEVQQASLADVDKAVEAAQAGFLVWSAMSGAERGRILMRAVAILRERNDELAM 84 Query: 103 LEVINNGKTITEAE-YDIDAAWQCIEYYAGLAPTLSGQHIQLPGGAFAYTRREPLGVCAG 161 LEV++ GK + EA DI IE+YAGLA T+ GQ L G F Y+RREPLGVCAG Sbjct: 85 LEVLDTGKPLQEANCVDIATGADVIEFYAGLAATIHGQQQDLGGTNFYYSRREPLGVCAG 144 Query: 162 ILAWNYPFMIAAWKCAPALACGNAVVFKPSPMTPVTGVILAEIFHEAGVPVGLVNVVQGG 221 I AWNYP IA WK PALA GN ++FKPS TP++ + LAEIF EAG+P G+ NV+QG Sbjct: 145 IGAWNYPIQIAMWKSGPALAAGNCMIFKPSEETPLSVMKLAEIFTEAGLPDGVFNVIQGD 204 Query: 222 AETGSLLCHHPNVAKVSFTGSVPTGKKVMEMSAKTVKHVTLELGGKSPLLIFKDCELENA 281 G L HP +AKVSFTG TGKKV+ +A ++K VT+ELGGKSPLL+F D +L+NA Sbjct: 205 YRAGQALSRHPQIAKVSFTGECGTGKKVVADAASSLKQVTMELGGKSPLLVFGDADLDNA 264 Query: 282 VRGALMANFLTQGQVCTNGTRVFVQREIMPQFLEEVVKRTKAIVVGDPLLTETRMGGLIS 341 V GAL+ANF TQG+VCTNGTRVFV I +F+ +VV RT+ +V+GDP T++G LIS Sbjct: 265 VSGALLANFYTQGEVCTNGTRVFVHDSIYDEFVSKVVARTERMVIGDPTDLNTQVGALIS 324 Query: 342 KPQLDKVLGFVAQAKKEGARVLCGGEPLTPSDPKLKNGYFMSPCVLDNCRDDMTCVKEEI 401 + + KVLGF+ AK GAR+ CGGE + + L GYF+ P V +C DDM VKEEI Sbjct: 325 EDHMHKVLGFIEAAKTAGARLACGGERVIANG--LDKGYFVQPTVFADCTDDMPNVKEEI 382 Query: 402 FGPVMSVLPFDTEEEVLQRANNTTFGLASGVFTRDISRAHRVAANLEAGTCYINTYSISP 461 FGPVMS+L F EEEV++RAN+T +GLA+GVF+ + SRAHRV A LEAG C+INT+ SP Sbjct: 383 FGPVMSILRFSDEEEVIRRANDTEYGLAAGVFSTNFSRAHRVIARLEAGICWINTWGASP 442 Query: 462 VEVPFGGYKMSGFGRENGQATVDYYSQLKTVIVEMGDVD 500 E+P GGYK SG GRENG T+++Y+Q+K+V VE+GDVD Sbjct: 443 AEMPVGGYKQSGIGRENGIETLNHYTQIKSVFVELGDVD 481 Lambda K H 0.319 0.135 0.404 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: 690 Number of extensions: 22 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: 503 Length of database: 484 Length adjustment: 34 Effective length of query: 469 Effective length of database: 450 Effective search space: 211050 Effective search space used: 211050 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 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