Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= BRENDA::A0A0E3T3B5 (503 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 320 bits (820), Expect = 7e-92 Identities = 185/479 (38%), Positives = 271/479 (56%), Gaps = 22/479 (4%) Query: 11 FIDGEWREPVLKKRI-PIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWALA 69 ++DG W +P R+ +INPATEQ+ G + A+D A++AA KA WA Sbjct: 8 YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPA-----WAAT 62 Query: 70 PGAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEAAWDIDDVSGC--FEYYADLAEG 127 P A R + L + A R EIA+ +++ G PL+ A +G F+ LA+ Sbjct: 63 PLAERLEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKT 122 Query: 128 LDAQQKTPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPS 187 +++ +L V+KEP+GVV LITPWN+P+ KVAPALAAGCA +LKPS Sbjct: 123 YAFERRQGTTL--------VVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPS 174 Query: 188 ELASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIM 247 E A + LA++ E G+P GV N++ G G E G L+SHP VD ++ TGS + GS +M Sbjct: 175 EFAPYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVM 234 Query: 248 TAAAQLVKPVSLELGGKSPIVVFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIA 307 A +K VSLELGGKS ++ D D KA + GQ C+A SRL + + Sbjct: 235 REGAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRL 294 Query: 308 AKFLDRLVQWCKNIKIADPLEEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGG-ARP 366 + + C IK+ DP + +GP+ +G Q++K+ + I T EGA+++ GG RP Sbjct: 295 DEAEGLAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERP 354 Query: 367 EHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVI 426 E L KG+F+ PT+ + VT +M I REE+FGPVL ++ ++ D+A+ AND YGL V Sbjct: 355 EGLDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVY 414 Query: 427 SKDLERCERVSKALQAGIVWIN--CSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVK 483 + DL+ V++ L+ G+V +N S P P+GG ++SG GRE G+ G + +L K Sbjct: 415 AGDLDEARAVARRLRTGMVHLNGALSHP---GGPFGGIRQSGVGREWGEAGFEEFLESK 470 Lambda K H 0.319 0.136 0.419 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: 662 Number of extensions: 41 Number of successful extensions: 6 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: 503 Length of database: 479 Length adjustment: 34 Effective length of query: 469 Effective length of database: 445 Effective search space: 208705 Effective search space used: 208705 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 (21.7 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