Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate WP_090445819.1 BLS63_RS14555 betaine-aldehyde dehydrogenase
Query= BRENDA::P49189 (494 letters) >NCBI__GCF_900100495.1:WP_090445819.1 Length = 490 Score = 487 bits (1254), Expect = e-142 Identities = 247/481 (51%), Positives = 332/481 (69%), Gaps = 5/481 (1%) Query: 17 GARVEPADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRI 76 G R PA + + + PATG V+A + + +V AV +A A K+W+ + M+R RI Sbjct: 12 GGRYVPASSGASFETVNPATGEVLARVQRASQADVERAVASAAAGQKVWAAMTAMQRSRI 71 Query: 77 LLEAARIIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLP 135 L A I+RER DE+A +E ++ GK + E R +DI LEYYAGL ++ GE I L Sbjct: 72 LRRAVEILRERNDELAELETLDTGKPLSETRFVDIVTGADVLEYYAGLVPAIEGEQIPLR 131 Query: 136 GGSFGYTRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEI 195 SF YTRREPLGV GIGAWNYP QIA WKSAPALA GNAM+FKPS TP+S L LAEI Sbjct: 132 ETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLSVLKLAEI 191 Query: 196 YSEAGVPPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIM-EMSAKGIKPVTL 253 YSEAG+P G+FNV+ G G GQ+L +HP + K+SFTG TG K+M S+ +K VT+ Sbjct: 192 YSEAGLPDGVFNVLTGSGREVGQWLTEHPGIEKISFTGGTSTGKKVMASASSSSLKEVTM 251 Query: 254 ELGGKSPLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQ 313 ELGGKSPLI+F D D++ A A+MANF + GQVC NGTRVFV + + +F +V+++ + Sbjct: 252 ELGGKSPLIVFEDADLDRAADIAVMANFYSSGQVCTNGTRVFVPRMLQARFEAKVLERVK 311 Query: 314 RIKIGDPLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYM 373 RI++GDP +T GPL++ H+E VLG++ +++GA++L GG D + G Y+ Sbjct: 312 RIRLGDPQDANTNFGPLVSFAHMESVLGYIDKGRQEGARLLIGGARVT--DGEYAKGAYV 369 Query: 374 RPCVLTNCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHR 433 P V T+C D+M V+EEIFGPVMSIL +D+E EV+ RAND+ +GLAAGV TRD+ RAHR Sbjct: 370 APTVFTDCSDEMCIVREEIFGPVMSILVYDSEDEVIRRANDSDYGLAAGVVTRDLARAHR 429 Query: 434 VVAELQAGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESA 493 V+ +L+AG C+IN + SP E+P GGYK+SG GRENG T+ +Y+++K+V VE+G S Sbjct: 430 VIHKLEAGICWINTWGESPAEMPVGGYKQSGVGRENGLTTLAHYTRIKSVQVELGGYSSV 489 Query: 494 F 494 F Sbjct: 490 F 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: 675 Number of extensions: 26 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 24 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