Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 486 bits (1250), Expect = e-141 Identities = 255/473 (53%), Positives = 323/473 (68%), Gaps = 9/473 (1%) Query: 24 DASGTE-KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82 D +GT ATG IAT + V A+ AKAA K W++ +G ER RIL AA Sbjct: 20 DTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTERGRILRRAAD 79 Query: 83 IIREREDEIATMECINNGKSIFEARL-DIDISWQCLEYYAGLAASMAGEHIQLPGGSFGY 141 I+RER +++ +E + GK + E + D LEY+ GLAAS+ GEHI L G + Y Sbjct: 80 IMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEHIPL-GEDWVY 138 Query: 142 TRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGV 201 T+RE LG+CVGIGAWNYP QIA WK APALACGN+MVFKPS TP+ AL +AEI EAG Sbjct: 139 TKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALKVAEILIEAGA 198 Query: 202 PPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPL 261 P G+FNVVQG G L P V KVS TGSVPTG K+ +A+G+K VT+ELGGKSPL Sbjct: 199 PAGVFNVVQGMGEVGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGMKHVTMELGGKSPL 258 Query: 262 IIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPL 321 IIF D D++NAV GA+ NF + GQVC NGTRVFVQK I +KF + ++T +GDP+ Sbjct: 259 IIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARLAERTGNAILGDPM 318 Query: 322 LEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNC 381 E T GP++ + VLG+++ KE+GA+++CGG DGY++ P V + Sbjct: 319 DEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGG------RRADMDGYFIEPTVFADV 372 Query: 382 RDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAG 441 DDMT +EEIFGPVMS+L FDTE EV+ RANDT FGL+AGVFT+D RAHRV+ L+AG Sbjct: 373 TDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHRVIGNLEAG 432 Query: 442 TCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494 +CFIN+YN +PVE PFGG K SG GREN + I+++SQ+K+V V MGDVE+AF Sbjct: 433 SCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRMGDVEAAF 485 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: 704 Number of extensions: 37 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: 485 Length adjustment: 34 Effective length of query: 460 Effective length of database: 451 Effective search space: 207460 Effective search space used: 207460 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 17 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