Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_008508467.1 BIBO1_RS14100 betaine-aldehyde dehydrogenase
Query= SwissProt::Q19A30 (505 letters) >NCBI__GCF_000182725.1:WP_008508467.1 Length = 487 Score = 485 bits (1248), Expect = e-141 Identities = 242/467 (51%), Positives = 326/467 (69%), Gaps = 10/467 (2%) Query: 41 PVFEPATGRVLCQMVPCGAEEVDEAIMSAHAAYVQWSKKSGTERARVMLEAARIIRERRE 100 PV PAT + + ++ A +A A +W+ ER R++ A I+RE+ Sbjct: 25 PVIYPATSEEIASLYSATPGIIEAAYAAALKAQGEWAALKPVERGRILRRTAEILREKNR 84 Query: 101 KIAKLEVINNGKSITEALV-DIDVAWQCIEYYAGVAGTLAGQHFQLPGGAFAYTRREPLG 159 K++KLE ++ GK++ E LV D A +E++ G+ G+ +L GG+FAYTRRE LG Sbjct: 85 KLSKLETLDTGKALQETLVADAASAADALEFFGGIISGFNGEFVEL-GGSFAYTRREALG 143 Query: 160 VCVGIGAWNYPFQIAACKSAPALACGNAMVFKPSPFTPVTAVILAEIYKEAGVPDGLFCV 219 +CVGIGAWNYP QIAA KSAPALA GNA +FKPS TP++A+ LAE YKEAG+PDGLF V Sbjct: 144 ICVGIGAWNYPIQIAAWKSAPALAMGNAFIFKPSENTPLSALALAEAYKEAGLPDGLFNV 203 Query: 220 VQGGAETGSLLCNHPKVAKVSFTGSVPTGKKVMEMSAKGVKQVTLELGGKSPLIIFKDCD 279 VQG + G+ L NH AKVS TGSVPTG+++M + + +K VT+ELGGKSPLI+F D D Sbjct: 204 VQGYGDVGAALVNHRLTAKVSLTGSVPTGRRIMAQAGEQLKHVTMELGGKSPLIVFDDAD 263 Query: 280 LENAVKGALMANFLTQGQVCCNGTRVFVHKDILPQFLEEVVKRTKAIAVGDPLLDSTRMG 339 LE+A+ GA++ NF + GQVC NGTRVFVHK+I +F+E +V+RT+ I +GDP ++T+MG Sbjct: 264 LESAIGGAMLGNFYSTGQVCSNGTRVFVHKNIRERFIERLVERTRKIRIGDPFDEATQMG 323 Query: 340 ALITKPHLEKVLGFVRQAKKEGGRVLCGGEPFVPSDPKLKG---GYFMSPCILDNCRDDM 396 LI+ +KVL ++++ K EG + CGG PKL+G G+F+ P + + D M Sbjct: 324 PLISAAQRDKVLSYIKKGKAEGATLACGG-----GVPKLQGFDKGFFIEPTVFTDVTDTM 378 Query: 397 TCVKEEIFGPVMSVLPFDTEEEVIRRANNTTFGLASGVFTRDISRAHRVAASLEAGTCFI 456 T +EEIFGP+MSVL F E+EVI RAN++ FGLA+GVFT D+SR HRV ++AGTC+I Sbjct: 379 TIAREEIFGPLMSVLEFSDEDEVIARANDSEFGLAAGVFTADLSRGHRVIGQIKAGTCWI 438 Query: 457 NNYNISPVEVPFGGYKMSGFGRENGQVTIEYYSQLKTVVVETGDVEN 503 N YN++PVEVPFGGYK SG GRENG + +YSQ+KTV VE G V++ Sbjct: 439 NAYNLTPVEVPFGGYKQSGIGRENGIAALAHYSQIKTVYVEMGKVDS 485 Lambda K H 0.320 0.136 0.410 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: 678 Number of extensions: 16 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: 505 Length of database: 487 Length adjustment: 34 Effective length of query: 471 Effective length of database: 453 Effective search space: 213363 Effective search space used: 213363 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