Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 348 bits (893), Expect = e-100 Identities = 196/472 (41%), Positives = 280/472 (59%), Gaps = 12/472 (2%) Query: 19 PILNKR-IPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARY 77 P L+ R +P +P+TE ++ + P + D+ AV +A+RA + W + R + Sbjct: 32 PALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQRAF---DSHVWRGLRPADREKL 88 Query: 78 LRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFE---YYAGLAEELDSKQ-K 133 L ++ I+ DEL LE++ GK + +A DV A E Y AG A +L+ + Sbjct: 89 LFRLSELIERHADELSALETLQSGKL--QGIARAIDVQAGAEFVRYMAGWATKLEGQTLD 146 Query: 134 APISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVT 193 I +P + +Y +EP+GVV I PWN+P +A WKIAPALAAGC +LKPSE +T Sbjct: 147 NSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLT 206 Query: 194 CLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQL 253 L L + E G+P GVLN+V G G AGA+L +HP V K+SFTGS+A G + A + Sbjct: 207 ALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGKVVGHAAVEN 266 Query: 254 VKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDK 313 + +LELGGKSP VV ED D +VA+ G FF GQ+C+A+SRL+VH S+ +D+ Sbjct: 267 MARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLDE 326 Query: 314 LVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGY 373 L A+ ++I + + GP+ S+A + +V++ I+SAK+EGAT++ GG R G Sbjct: 327 LAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEGATLVAGGERVH--DAGC 384 Query: 374 FVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERC 433 FV+PTI D T M++ REEVFGPVLAV F E+AI ANDT YGL +++ + L Sbjct: 385 FVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHA 444 Query: 434 ERLSKALQAGIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 R+ LQAG+VW+N P GGIK+SG GR+LG +E + +K V Sbjct: 445 HRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496 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: 524 Number of extensions: 20 Number of successful extensions: 2 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: 500 Length adjustment: 34 Effective length of query: 469 Effective length of database: 466 Effective search space: 218554 Effective search space used: 218554 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 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