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_086509897.1 BZY95_RS10630 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9JLJ3 (494 letters) >NCBI__GCF_002151265.1:WP_086509897.1 Length = 489 Score = 463 bits (1191), Expect = e-135 Identities = 233/478 (48%), Positives = 317/478 (66%), Gaps = 4/478 (0%) Query: 19 RVEPVDASGTEKAFEPATGREIATFKCSGEKEVNLAVENAKAAFKIWSKKSGLERCQVLL 78 R EP + T P G +A + + +++ AV +A + W+ +G++R +VL Sbjct: 14 RREPATSGETFDVLNPYDGSLLARVDQASQADIDRAVASASQGQRRWAAMTGMQRGRVLQ 73 Query: 79 EAARIIKERRDEIAIMETINNGKSIFE-ARLDVDTSWQCLEYYAGLAASMAGEHIQLPGG 137 A +++ER DE+A +ET N GK I E A +D+ T LEYYAGLA ++ G I L Sbjct: 74 RAVALLRERNDELAELETRNTGKPISETAAVDIVTGADVLEYYAGLAPAIEGAQIPLRES 133 Query: 138 SFGYTRREPLGVCLGIGAWNYPFQIACWKSAPALACGNAMIFKPSPFTPVSALLLAEIYT 197 SF YTRREPLGV IGAWNYP QIACWK+APALA GNA++FKPS TP++A+ LAEI+T Sbjct: 134 SFVYTRREPLGVIAAIGAWNYPIQIACWKAAPALAAGNAVVFKPSEVTPLTAMKLAEIFT 193 Query: 198 KAGAPNGLFNVVQGGAATGQFLCQHRDVAKVSFTGSVPTGMKIMEMA-AKGIKPITLELG 256 + G P+G+FNVV G A GQ L H +AKVSFTG V TG K+M A +K +T+ELG Sbjct: 194 EVGLPDGVFNVVHGEARVGQMLTAHEGIAKVSFTGEVGTGKKVMAAAGGSTLKDVTMELG 253 Query: 257 GKSPLIIFSDCNMKNAVKGALLANFLTQGQVCCNGTRVFVQKEIADAFTKEVVRQTQRIK 316 GKSPLI+F+D ++ A A++ANF + GQ+C NGTRVFV++ + AF +++V + RI+ Sbjct: 254 GKSPLIVFADADLDRAADAAMMANFYSSGQICTNGTRVFVERSVKAAFEEKIVERVARIR 313 Query: 317 IGDPLLEDTRMGPLINAPHLERVLGFVRSAKEQGATVLCGGEPYAPEDPKLKHGYYMTPC 376 GDPL + GPL++ H +VL ++ K+ GA VL GGEP ++ G + Sbjct: 314 AGDPLDPEINFGPLVSFEHQAKVLDYIAYGKQDGARVLIGGEPL--DEGDFARGAWAPAT 371 Query: 377 ILTNCTDDMTCVKEEIFGPVMSILTFETEAEVLERANDTTFGLAAGVFTRDIQRAHRVAA 436 + T+C+D+M V+EEIFGPVMSIL F+ E E++ RANDT +GLAAGVFT + RAHR Sbjct: 372 VFTDCSDEMRIVREEIFGPVMSILVFDDEEELIRRANDTHYGLAAGVFTESLARAHRTIH 431 Query: 437 ELQAGTCYINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494 ++AG C+IN + SP E+P GGYK+SG GRENG T+ +Y+Q K+V VEMG ES F Sbjct: 432 RMEAGICWINTWGESPAEMPVGGYKQSGVGRENGIETLAHYTQTKSVQVEMGPFESVF 489 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: 686 Number of extensions: 24 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: 489 Length adjustment: 34 Effective length of query: 460 Effective length of database: 455 Effective search space: 209300 Effective search space used: 209300 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