Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_076476004.1 BW971_RS02050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_900156495.1:WP_076476004.1 Length = 500 Score = 392 bits (1008), Expect = e-113 Identities = 225/471 (47%), Positives = 291/471 (61%), Gaps = 14/471 (2%) Query: 56 RWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSLLRKW 115 R T TF V DPA+G +L VAD G +A A++ + A W S +ERS +LR Sbjct: 32 RTAATARTFVVDDPATGRELTQVADAGPDDAMLALKQSVAAADDWAATSPRERSVILRAA 91 Query: 116 YDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSAKDKR 175 +DL+ + +LA ++T E GK L +++ EI Y A FL WFSEEA R+ G + R Sbjct: 92 FDLITERAADLALLMTLEMGKALPDSKSEIAYGAEFLRWFSEEAVRINGRYTQSPGGTGR 151 Query: 176 GLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQLANQA 235 LV QPVG ITPWNFP AM TRK+G ALAAG T++VKPA +TP + LALA++ +A Sbjct: 152 ILVTHQPVGPCLAITPWNFPLAMGTRKIGPALAAGNTIIVKPAAETPLTMLALAKIFAEA 211 Query: 236 GIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRVSMEL 295 G+PPGV V+P S A V L D + KI+FTGST G+ILL AA +V+R SMEL Sbjct: 212 GLPPGVLAVLPTS--DASAVCTPLIEDTRIRKITFTGSTGVGRILLGQAAANVQRTSMEL 269 Query: 296 GGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAE---AM 352 GG APFIVFD A++D A+ GA A+K RN G+ C +NRFLV HDS +F + A Sbjct: 270 GGNAPFIVFDDADLDAALDGAFAAKMRNGGEACTAANRFLV----HDSVAEEFTDGLIAR 325 Query: 353 KKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG-----KRHQSGGNF 407 ++L VG G+ +GTT GPLI+EK V + V DAVA GA V GG ++H G F Sbjct: 326 MQALTVGPGYADGTTLGPLISEKQRNSVAQKVTDAVADGARVRLGGEQARAEQHGGDGWF 385 Query: 408 FEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIW 467 + PT+L V E FGPVA + F +EA+A AN + GLA Y Y++D + Sbjct: 386 YPPTVLDEVPVGAEITRGEIFGPVAVISTFGTVDEAIAAANDTEYGLAAYIYTRDLDRAL 445 Query: 468 RVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518 V+++L+ G+VGVN G+IS V PFGG KQSGLGREG GI E+L KYV Sbjct: 446 SVSDRLQTGLVGVNRGVISDVAAPFGGEKQSGLGREGGLEGIGEFLTTKYV 496 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: 599 Number of extensions: 23 Number of successful extensions: 4 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: 500 Length adjustment: 35 Effective length of query: 488 Effective length of database: 465 Effective search space: 226920 Effective search space used: 226920 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