Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085770042.1 B1812_RS01610 aldehyde dehydrogenase family protein
Query= BRENDA::G5DDC2 (506 letters) >NCBI__GCF_002117405.1:WP_085770042.1 Length = 474 Score = 312 bits (799), Expect = 2e-89 Identities = 184/483 (38%), Positives = 270/483 (55%), Gaps = 25/483 (5%) Query: 12 QLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWAR 71 + ++DG W PA+ R L V+NP TEA G I G+A DVD AVAAA A K ++R Sbjct: 6 KFYIDGHWVEPAELRTLEVINPATEAVCGHIALGSATDVDRAVAAAGEAFK-----SFSR 60 Query: 72 APGAVRAKYLRAIAAKVIERKQELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEAL 131 R + L+ I ++ +R +++A+ + G P A + +F+ E L Sbjct: 61 TSRRERLELLQRIVVELEKRHEDMARAITEEMGAPVWLAQRAQARMGAA--HFSTAIEVL 118 Query: 132 -----DKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKVAPALAAGCAAV 186 ++R+ + + + +EPIGV G ITPWN+PL K+APALA GCA V Sbjct: 119 KRYEFEERRGATIIV----------KEPIGVCGFITPWNWPLNQMACKIAPALATGCAMV 168 Query: 187 LKPSELASVTCLELADICKEVGLPPGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETG 246 LKPSE+A + + LA+ + G PPGV N+V G GP GA +S+HP V V+FTGS G Sbjct: 169 LKPSEIAPFSGIVLAEALEAAGTPPGVFNLVNGDGPTVGAAISSHPGVSMVSFTGSTRAG 228 Query: 247 KKIMAAAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLVH 306 ++ AAP VK + ELGGKSP ++ +D D+ AV + +GQ C+A +R+L Sbjct: 229 VEVAKNAAPTVKRICQELGGKSPNILLEDADMKAAVTAGVNAVMLNSGQSCNAPTRMLAP 288 Query: 307 TKIAKEFNEKMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGG 366 K +E + A+ V DP ++GPVVSE Q+ K++ I EGA+++ GG Sbjct: 289 RKRMEEVIGFARSAAEATTVGDP-NGNAQMGPVVSEAQWNKVQGLIQKGLEEGASLVAGG 347 Query: 367 V-RPAHLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLA 425 + +P LEKG++++PT+ ++T M I REE+FGPVL + + +AIE+ANDT+YGL+ Sbjct: 348 LGKPEGLEKGYYVKPTVFANVTNDMTIAREEIFGPVLSILAYDRVADAIEIANDTEYGLS 407 Query: 426 GAVISGDRERCQRLSEEIDAGIIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSV 485 V D R + + AG + +N S P AP+GG K SG GRE G+ +L Sbjct: 408 AYVSGADPARLMETASRLRAGQVQLN-SAPMDLMAPFGGYKMSGNGREWGDHAFAEFLET 466 Query: 486 KQV 488 K + Sbjct: 467 KAI 469 Lambda K H 0.318 0.135 0.421 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: 581 Number of extensions: 32 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: 506 Length of database: 474 Length adjustment: 34 Effective length of query: 472 Effective length of database: 440 Effective search space: 207680 Effective search space used: 207680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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