Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__Putida:PP_5063 Length = 490 Score = 486 bits (1250), Expect = e-141 Identities = 253/484 (52%), Positives = 334/484 (69%), Gaps = 6/484 (1%) Query: 14 YRGGARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMER 73 Y GA V+ A + T +A PATG V+A + E +V AV++A+ K+W+ + M+R Sbjct: 10 YIDGAYVD-AGSDATFEAINPATGEVLAHVQRATEADVEKAVESAERGQKVWAAMTAMQR 68 Query: 74 CRILLEAARIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHI 132 RIL A I+RER DE+A +E ++ GKS E R +DI LEYYAGL ++ GE I Sbjct: 69 SRILRRAVDILRERNDELAMLETLDTGKSYSETRYVDIVTGADVLEYYAGLVPAIEGEQI 128 Query: 133 QLPGGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLL 192 L SF YTRREPLGV VGIGAWNYP QIA WKSAPALA GNAM+FKPS T ++ L L Sbjct: 129 PLRESSFVYTRREPLGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKL 188 Query: 193 AEIYSEAGVPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIM-EMSAKGIKP 250 AEIY+EAG+P G+FNV+ G G G +L +HP + KVSFTG TG K+M S+ +K Sbjct: 189 AEIYTEAGLPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMASASSSSLKE 248 Query: 251 VTLELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVK 310 VT+ELGGKSPLII +D D++ A A+MANF + GQVC NGTRVF+ E+ F ++ + Sbjct: 249 VTMELGGKSPLIICADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEMKAAFEAKIAE 308 Query: 311 QTQRIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDG 370 + RI++G+P E+T GPL++ H+E VLG++ KE+GA+VLCGG+ D G Sbjct: 309 RVARIRVGNPEDENTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERLTAGD--FAKG 366 Query: 371 YYMRPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQR 430 ++ P V T+C DDMT VKEEIFGPVMSIL+++TE EV+ RANDT +GLAAGV T DI R Sbjct: 367 AFVAPTVFTDCTDDMTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAGVCTNDITR 426 Query: 431 AHRVVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDV 490 AHR++ +L+AG C+IN + SP E+P GGYK+SG GRENG ++ Y+++K+V VE+G Sbjct: 427 AHRIIHKLEAGICWINAWGESPAEMPVGGYKQSGVGRENGVSSLAQYTRIKSVQVELGGY 486 Query: 491 ESAF 494 S F Sbjct: 487 NSVF 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: 696 Number of extensions: 30 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