Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate SMc00094 SMc00094 betaine aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__Smeli:SMc00094 Length = 487 Score = 456 bits (1172), Expect = e-132 Identities = 241/474 (50%), Positives = 321/474 (67%), Gaps = 7/474 (1%) Query: 24 DASGTE-KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82 DA+GT ++ PATG +IA + V A+ AK A W+ S R RIL AA Sbjct: 18 DAAGTVIESIYPATGEIIARLHAATPGIVEKAIAAAKRAQPEWAAMSPTARGRILKRAAE 77 Query: 83 IIREREDEIATMECINNGKSIFEARL-DIDISWQCLEYYAGLA-ASMAGEHIQLPGGSFG 140 ++R+R E++ +E ++ GK I E + D E++ G+A A++ G++I L GG F Sbjct: 78 LMRQRNRELSELETLDTGKPIQETIVADPTSGADSFEFFGGVAPAALNGDYIPL-GGDFA 136 Query: 141 YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAG 200 YT+R PLGVCVGIGAWNYP QIA WK APAL GNAMVFKPS TP+ AL +AEI EAG Sbjct: 137 YTKRVPLGVCVGIGAWNYPQQIACWKGAPALVAGNAMVFKPSENTPLGALKIAEILIEAG 196 Query: 201 VPPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSP 260 +P GLFNV+QG ATG L HPDVAKVS TGSVPTG K+ +A +K VT+ELGGKSP Sbjct: 197 LPKGLFNVIQGDRATGPLLVNHPDVAKVSLTGSVPTGKKVAGAAAAELKHVTMELGGKSP 256 Query: 261 LIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDP 320 LI+F D D+ +A+ GA++ NF + GQVC NGTRVFVQ++I + F + ++T+ I IGDP Sbjct: 257 LIVFDDADLESAIGGAMLGNFYSTGQVCSNGTRVFVQRKIKEPFLARLKERTEAIVIGDP 316 Query: 321 LLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTN 380 L E T++GP+++ ++V ++ K +GA+++ GG I P + +G Y++P V + Sbjct: 317 LDEATQLGPMVSAAQRDKVFSYIGKGKAEGARLVTGGGI--PNNVS-GEGTYIQPTVFAD 373 Query: 381 CRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQA 440 D MT +EEIFGPVM +L FD E EV+ RAN T FGL+AGVFT D+ RAHRV L+A Sbjct: 374 VTDGMTIAREEIFGPVMCVLDFDDEVEVIARANATEFGLSAGVFTADLTRAHRVADRLEA 433 Query: 441 GTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494 GT +IN YN+ PVE+PFGG K+SGFGREN + +Y++LKTV V MG VE+ + Sbjct: 434 GTLWINTYNLCPVEIPFGGSKQSGFGRENSVAALNHYTELKTVYVGMGPVEAPY 487 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: 651 Number of extensions: 34 Number of successful extensions: 3 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: 487 Length adjustment: 34 Effective length of query: 460 Effective length of database: 453 Effective search space: 208380 Effective search space used: 208380 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