Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__WCS417:GFF5142 Length = 490 Score = 481 bits (1238), Expect = e-140 Identities = 245/475 (51%), Positives = 330/475 (69%), Gaps = 5/475 (1%) Query: 23 ADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82 A + T +A PA G V+A + +++V AV +A+ KIW+ + MER RIL A Sbjct: 18 AGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEKGQKIWAAMTAMERSRILRRAVD 77 Query: 83 IIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFGY 141 I+RER DE+A +E ++ GK+ E + +DI LEYYAGL ++ GE I L SF Y Sbjct: 78 ILRERNDELAALETLDTGKAFSETKYVDIVTGADVLEYYAGLVPAIEGEQIPLRDTSFVY 137 Query: 142 TRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGV 201 TRREPLGV GIGAWNYP QIA WKSAPALA GNAM+FKPS T ++ L LAEIY+EAGV Sbjct: 138 TRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGV 197 Query: 202 PPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIM-EMSAKGIKPVTLELGGKS 259 P G+FNV+ G G G +L +HP + KVSFTG TG K+M S+ +K VT+ELGGKS Sbjct: 198 PAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSSLKEVTMELGGKS 257 Query: 260 PLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGD 319 PLI+F D D++ A A+MANF + GQVC NGTRVFV K + F ++V++ RI++G+ Sbjct: 258 PLIVFEDADLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEAKIVERVARIRVGN 317 Query: 320 PLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLT 379 P ++T GPL++ H+E VLG++ KE+GA+VLCGGD D + G ++ P V T Sbjct: 318 PQDDNTNFGPLVSFAHMESVLGYIAKGKEEGARVLCGGDRLT--DGEFAKGAFVAPTVFT 375 Query: 380 NCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQ 439 +C D+MT V+EEIFGPVMSIL+++TE EV+ RANDT FGLAAG+ T+D+ RAHRV+ +L+ Sbjct: 376 DCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKDLNRAHRVIHQLE 435 Query: 440 AGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494 AG C+IN + S ++P GGYK+SG GRENG ++ ++++K+V VE+GD S F Sbjct: 436 AGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVELGDYASVF 490 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: 689 Number of extensions: 31 Number of successful extensions: 5 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: 490 Length adjustment: 34 Effective length of query: 460 Effective length of database: 456 Effective search space: 209760 Effective search space used: 209760 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