Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; Gamma-aminobutyraldehyde dehydrogenase; EC 1.2.1.47; EC 1.2.1.3; EC 1.2.1.19 (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9JLJ3 (494 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 466 bits (1200), Expect = e-136 Identities = 238/490 (48%), Positives = 327/490 (66%), Gaps = 17/490 (3%) Query: 6 FVVSQPLNYRGGARVEPVDASGTEKAFEPATGREIATFKCSGEKEVNLAVENAKAAFKIW 65 FV +PL GA + + PATG EIA + + A+ + A W Sbjct: 10 FVDGRPLEDETGAPIPVI---------YPATGEEIARLHEATPAVIEAALASGARAQAAW 60 Query: 66 SKKSGLERCQVLLEAARIIKERRDEIAIMETINNGKSIFEARL-DVDTSWQCLEYYAGLA 124 + +ER ++L A+ +I+ R +E++++ET++ GK + E + D + LE++AGLA Sbjct: 61 AAMRPVERARILRRASDLIRARNEELSLLETLDTGKPLQETLVADWASGADALEFFAGLA 120 Query: 125 ASMAGEHIQLPGGSFGYTRREPLGVCLGIGAWNYPFQIACWKSAPALACGNAMIFKPSPF 184 ++ GE + L G F YT REPLG+C+GIGAWNYP QIACWK+APALA GNAM+FKPS Sbjct: 121 PAVTGETVPL-GQDFVYTIREPLGLCVGIGAWNYPSQIACWKAAPALALGNAMVFKPSEV 179 Query: 185 TPVSALLLAEIYTKAGAPNGLFNVVQGGAATGQFLCQHRDVAKVSFTGSVPTGMKIMEMA 244 TP+ AL LAEI +AG P GLFNVVQG A G L VAKVS TGSVPTG ++ A Sbjct: 180 TPLGALKLAEILIEAGLPPGLFNVVQGRGAVGAALVTDSRVAKVSLTGSVPTGRRVYAAA 239 Query: 245 AKGIKPITLELGGKSPLIIFSDCNMKNAVKGALLANFLTQGQVCCNGTRVFVQKEIADAF 304 A+G++ +T+ELGGKSPLI+F D ++++A+ A+L NF + GQ+C NGTRVFVQK I +AF Sbjct: 240 AEGVRHVTMELGGKSPLIVFDDADLESAIGAAMLGNFYSAGQICSNGTRVFVQKGIKEAF 299 Query: 305 TKEVVRQTQRIKIGDPLLEDTRMGPLINAPHLERVLGFVRSAKEQGATVLCGGEPYAPED 364 + + I++GDPL + +MGPL++ LE+VL ++ A+ +G ++CGGE Sbjct: 300 LARLAERADAIRMGDPLDPEVQMGPLVSQAQLEKVLAYIEKARAEGGRLVCGGE------ 353 Query: 365 PKLKHGYYMTPCILTNCTDDMTCVKEEIFGPVMSILTFETEAEVLERANDTTFGLAAGVF 424 + G Y+ P + + TD MT +EE+FGPVM++L FETE E + RAN T FGLAAGVF Sbjct: 354 ASVSPGCYVQPTVFADVTDAMTLAREEVFGPVMAVLDFETEEEAIARANATDFGLAAGVF 413 Query: 425 TRDIQRAHRVAAELQAGTCYINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVC 484 T D+ RAHRV A+LQAGTC+IN YN++PVE PFGG K SG GRENGR +E+Y+Q+K+V Sbjct: 414 TADLTRAHRVVAQLQAGTCWINAYNLTPVEAPFGGVKLSGVGRENGRAAVEHYTQVKSVY 473 Query: 485 VEMGDVESAF 494 V MG V++ + Sbjct: 474 VGMGPVDAPY 483 Lambda K H 0.319 0.136 0.408 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: 667 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: 483 Length adjustment: 34 Effective length of query: 460 Effective length of database: 449 Effective search space: 206540 Effective search space used: 206540 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 10 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