Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_086510804.1 BZY95_RS15485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_002151265.1:WP_086510804.1 Length = 481 Score = 540 bits (1391), Expect = e-158 Identities = 265/482 (54%), Positives = 357/482 (74%), Gaps = 3/482 (0%) Query: 42 LHADLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 L AD+ +F+GG+W F V +PA+G L +V D +AR AV AA A+ +W+ Sbjct: 3 LPADIFSDKAFIGGQWRDAERRFDVTNPANGETLASVPDLSADDARDAVAAAEAAWPAWR 62 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 + K+R++LLR W+D ++ +++ LA+++T E GKPL E++GE+ Y A F+E+++E+A+R Sbjct: 63 RQTAKQRAALLRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFVEFYAEQAKR 122 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 + G+ + + DKR LV ++PVGV + ITPWNFP AMITRK ALAAGC VV+KPAE T Sbjct: 123 MAGETLPSHGADKRILVFREPVGVVAAITPWNFPLAMITRKCAPALAAGCPVVIKPAEAT 182 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 P +ALALA+LA Q G P GV NV+ SR E+GEVL +DP V K+SFTGSTA GK LL Sbjct: 183 PLTALALARLAEQVGFPAGVLNVVTASRPA--EIGEVLTSDPRVRKVSFTGSTAVGKRLL 240 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A +VK+ SMELGG APFIVFD A++D AV GA+ASK+RN+GQTCVC+NR LVQ G++ Sbjct: 241 AQCAGTVKKASMELGGNAPFIVFDDADLDAAVEGAVASKYRNSGQTCVCTNRLLVQSGVY 300 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 ++FV K A A L+VGNG +EG QGPLIN+ AV+KV+ H+ DA+AKGA +V GG+ H Sbjct: 301 EAFVEKLA-ARVAQLKVGNGLDEGVVQGPLINQAAVDKVQSHIADALAKGARLVCGGEPH 359 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 GG FF+PT++++VT +M EETFGP+APV +FD +E+A+A+ANA + GLA YFY++ Sbjct: 360 ALGGTFFQPTVVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMANATEFGLAAYFYAR 419 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 D +IW V E LE GMV VNEG++S+ PFGGVK+SGLGREGS +G+DE+ E+KYVC G Sbjct: 420 DYRRIWHVMEGLEYGMVAVNEGILSTELAPFGGVKESGLGREGSHHGLDEFTELKYVCVG 479 Query: 522 GL 523 GL Sbjct: 480 GL 481 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: 655 Number of extensions: 23 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: 481 Length adjustment: 34 Effective length of query: 489 Effective length of database: 447 Effective search space: 218583 Effective search space used: 218583 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