Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_029134020.1 A3GO_RS0114560 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000428045.1:WP_029134020.1 Length = 485 Score = 558 bits (1438), Expect = e-163 Identities = 264/482 (54%), Positives = 366/482 (75%), Gaps = 5/482 (1%) Query: 44 ADLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 ++LL+ +++ G W+ TF V +PA +++ V G E R A+ A AF W+ Sbjct: 4 SNLLKNQAYINGEWISADNGHTFAVTNPADNSEITRVPSLGAAETRRAIEQADLAFRCWR 63 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 + + +ERS+LLR+W++L++ N++ LA++++ E GKPL E++GEI Y A F+EWF+EEA+R Sbjct: 64 KRTAQERSNLLRRWFELIMANQEALAQLLSLEQGKPLAESRGEIAYGASFIEWFAEEAKR 123 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 VYGD+I A D+R +V+KQP+GV + ITPWNFP+AMITRK A+AAGCTVV+KPA DT Sbjct: 124 VYGDVIPAHAADRRFVVIKQPIGVVAAITPWNFPNAMITRKCAPAMAAGCTVVIKPAPDT 183 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 P SALALA LA++AGIPPGV+NV+P A VG L ++P+V K+SFTGSTA GK+L+ Sbjct: 184 PLSALALAALADEAGIPPGVFNVLPTENAVA--VGGELTSNPIVRKLSFTGSTAVGKLLM 241 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A +VK+VS+ELGG APF+VFD A++D AVAGA+ASK+RN+GQTCVC+NRFL+Q I+ Sbjct: 242 SQCAGTVKKVSLELGGNAPFLVFDDADIDAAVAGALASKYRNSGQTCVCTNRFLIQESIY 301 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 D F K A+ +L+VG + QGPLIN+ AVEKV++HV+DAVAKGA ++TGG+RH Sbjct: 302 DEFAEKLTRAV-DALQVGPALTSDSQQGPLINQAAVEKVQRHVDDAVAKGARLMTGGQRH 360 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 GG F++PT+L+ VTR+M EETFGPVAP+ F E+EA+ +AN GLA YFY++ Sbjct: 361 TLGGTFYQPTILAGVTREMHIACEETFGPVAPLFSFKTEQEAIDLANDTPFGLAAYFYAR 420 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 D ++WRVAE LE GM+G+NEG+IS+ PFGG+K+SG+GREGS+YG+D+++E+KY+C G Sbjct: 421 DIGRVWRVAEALETGMIGINEGIISTAVAPFGGIKESGIGREGSRYGMDDFIEMKYLCMG 480 Query: 522 GL 523 GL Sbjct: 481 GL 482 Lambda K H 0.318 0.135 0.400 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: 669 Number of extensions: 20 Number of successful extensions: 3 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: 523 Length of database: 485 Length adjustment: 34 Effective length of query: 489 Effective length of database: 451 Effective search space: 220539 Effective search space used: 220539 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