Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 467 bits (1202), Expect = e-136 Identities = 240/476 (50%), Positives = 327/476 (68%), Gaps = 7/476 (1%) Query: 24 DASGTE--KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAA 81 DAS E ++ PA G V+A +G ++ AV++A+ +IW+ +G+ER RI+ A Sbjct: 17 DASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTGIERARIMRRAV 76 Query: 82 RIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFG 140 ++RER DE+A +E ++ GK + E R +DI LEYYAGLA ++ GE I L SF Sbjct: 77 DLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQIPLRDSSFV 136 Query: 141 YTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAG 200 YTRREPLGV GIGAWNYP QIA WK+APALA GNAM+FKPS T +SAL LAEI+SEAG Sbjct: 137 YTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALKLAEIFSEAG 196 Query: 201 VPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKG-IKPVTLELGGK 258 +P G+FNV+ G GA G + +HP +AKVSFTG V TG K+M +A +K VT+ELGGK Sbjct: 197 LPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLKDVTMELGGK 256 Query: 259 SPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIG 318 SPLII D D++ A A+MANF + GQVC NGTRVFV + F +++++ QRI++G Sbjct: 257 SPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKLLERVQRIRLG 316 Query: 319 DPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVL 378 DP E+T GPL++ H+ VL ++ K GA++LCGG+ V E K G ++ P + Sbjct: 317 DPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGE-RVTEGEYAK-GAFVAPTIF 374 Query: 379 TNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAEL 438 ++C DDM V EEIFGPV+S+L + E EV+ RANDT +GLAAGV T D+ RAHR++ L Sbjct: 375 SDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLARAHRIIHRL 434 Query: 439 QAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494 +AG C+IN + SP ++P GGYK+SG GRENG ++ +Y+++K+V VE+G+ S F Sbjct: 435 EAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVELGEFASVF 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: 676 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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