Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate H281DRAFT_02464 H281DRAFT_02464 betaine aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__Burk376:H281DRAFT_02464 Length = 489 Score = 489 bits (1258), Expect = e-142 Identities = 248/483 (51%), Positives = 328/483 (67%), Gaps = 5/483 (1%) Query: 14 YRGGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMER 73 Y GG V+ A T +PA G +AT + +V+ AVQ+A+ + W+ +GM+R Sbjct: 10 YIGGTYVD-ATGGETFDTVDPANGETLATVQQASSADVDRAVQSAREGQREWAALTGMQR 68 Query: 74 CRILLEAARIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHI 132 RIL A I+RER DE+A +E + GK I E + +DI +EYYAGLA ++ G+ I Sbjct: 69 SRILRRAVDILRERNDELAALETRDTGKPIAETQAVDIVTGADVIEYYAGLATAIEGQQI 128 Query: 133 QLPGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLL 192 L SF YTRREPLGVC GIGAWNYP QIA WKSAPALA GNAM+FKPS TP+SAL L Sbjct: 129 PLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEVTPLSALKL 188 Query: 193 AEIYSEAGVPPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMS-AKGIKPV 251 AEIY+EAGVPPG+FNVVQG G L HPD+ K+SFTG V TG K+M M+ A +K V Sbjct: 189 AEIYTEAGVPPGVFNVVQGDGRVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLKEV 248 Query: 252 TLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQ 311 T+ELGGKSPL++F D ++ A A+ ANF + GQVC NGTRVFVQ+ +L++F V+++ Sbjct: 249 TMELGGKSPLLVFDDANLERAADIAMSANFFSSGQVCTNGTRVFVQRSVLERFEALVLER 308 Query: 312 TQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGY 371 +RI++G P T GPL++ L++VLG++ ++GA+++ GG + G Sbjct: 309 VKRIRVGAPGDASTNFGPLVSAAQLQKVLGYIDSGVQEGARLIAGGKRL--SEGHFGQGQ 366 Query: 372 YMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRA 431 Y+ P V T C DDM V+EEIFGPVMSIL FD E E +ERAN T +GLAAGV T ++ RA Sbjct: 367 YVEPTVFTGCHDDMRIVREEIFGPVMSILIFDNEDEAIERANRTAYGLAAGVVTENLARA 426 Query: 432 HRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVE 491 HRV+ L+AG C+IN + SP E+P GGYK+SG GRENG T+E+Y+++K+V VE+G + Sbjct: 427 HRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVELGPYQ 486 Query: 492 SAF 494 F Sbjct: 487 PVF 489 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: 687 Number of extensions: 31 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 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