Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 299 bits (765), Expect = 2e-85 Identities = 173/477 (36%), Positives = 276/477 (57%), Gaps = 10/477 (2%) Query: 17 GARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRI 76 G ++ PA + PATG +I T +++V++AV +AKAA K W+++S R ++ Sbjct: 23 GGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAAQKDWAKQSARARGKL 82 Query: 77 LLEAARIIREREDEIATMECINNGKSI-FEARLDIDISWQCLEYYAGLAASMAGEHIQLP 135 + E R++ +E+ + + GK++ E+R++ + ++ GL + + GE I Sbjct: 83 VAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETIPFN 142 Query: 136 GGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEI 195 T REP+GV I WN P + + K+A AL GN++V K + P++ L +AEI Sbjct: 143 PDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRVAEI 202 Query: 196 YSEAGVPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLE 254 + +PPGLFN++ G G G L +HPDV KV+FTGSV TG + + +A+ + PVTLE Sbjct: 203 MNTV-LPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVTLE 261 Query: 255 LGGKSPLIIFSDCDMNNAVKGALMA-NFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQ 313 LGGKSP+I+ +D DM+ AV GAL F QGQ C +R+FV + I D+F +V + Sbjct: 262 LGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAKVD 321 Query: 314 RIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKE-QGA-KVLCGGDIYVPEDPKLKDGY 371 + +GDPL E T +G +++ LERV ++K+ +E +GA K +C +P DPKL G Sbjct: 322 AMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSA---LPTDPKLAKGR 378 Query: 372 YMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRA 431 +++P + T ++ +EEIFGPV +++ + +VL +AND+ +GLAA ++TRD + A Sbjct: 379 FVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKLA 438 Query: 432 HRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENG-RVTIEYYSQLKTVCVEM 487 L+AG +N V L +GG K SG G+E +E+++ KT+ M Sbjct: 439 MDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKTIIFNM 495 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: 589 Number of extensions: 30 Number of successful extensions: 6 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: 496 Length adjustment: 34 Effective length of query: 460 Effective length of database: 462 Effective search space: 212520 Effective search space used: 212520 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