Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 335 bits (860), Expect = 2e-96 Identities = 200/479 (41%), Positives = 275/479 (57%), Gaps = 16/479 (3%) Query: 9 QLFIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSA 68 + +I G+W P N I NP+TE +I +P T D D A AA A W+A Sbjct: 6 RFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPA-----WAA 60 Query: 69 ASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEAL-ADLDDVVACFEYYAGLAEE 127 SG+ R +L+ IA +K ++DELG+L + + G P++ A + + F A +A E Sbjct: 61 LSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE 120 Query: 128 LDSKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPS 187 ++++ SL +LK P G VA ITPWN+P K+ ALAAGC +LKPS Sbjct: 121 GFAEERIGQSL--------VLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPS 172 Query: 188 ELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIM 247 E+A + L E+ + GLP GV N+VTG G G +LA+HP + +SFTGS+A G ++ Sbjct: 173 EVAPLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVA 232 Query: 248 TTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIA 307 AA VK VSLELGGKS VV D DL + TV GCF +GQ CSA +RL+V + Sbjct: 233 AVAAATVKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERY 292 Query: 308 VEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGG-RRP 366 E V+ A + DPL EG RLGP+VS Q ++V I A ++GA +L GG P Sbjct: 293 AEAAALAVQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAP 352 Query: 367 EHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVM 426 E L GY+V PT+ V + REEVFGPVLA+ T+ E EA +AN T YGL +AV Sbjct: 353 EGLPTGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVW 412 Query: 427 SNDLERCERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 S + R ++ L+AG V IN A + + AP+GG K+SG+GRELG G+E++L + + Sbjct: 413 SAEEARALAFARRLRAGQVDINGAFFNLL-APFGGFKQSGYGRELGRHGVEDFLETQSI 470 Lambda K H 0.317 0.134 0.402 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: 503 Number of extensions: 23 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: 503 Length of database: 476 Length adjustment: 34 Effective length of query: 469 Effective length of database: 442 Effective search space: 207298 Effective search space used: 207298 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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