Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_028586043.1 G494_RS0120720 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000429965.1:WP_028586043.1 Length = 473 Score = 422 bits (1085), Expect = e-122 Identities = 222/469 (47%), Positives = 308/469 (65%), Gaps = 7/469 (1%) Query: 52 FVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSL 111 F+ G WL FPV +PA+G + VA+ +A A+ AA AF +W + + ERS+L Sbjct: 2 FINGTWLERQDQFPVTNPANGELIAQVANGTREDAATAIAAAAAAFPAWSQTTSYERSAL 61 Query: 112 LRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSA 171 L + + LM + ++ELA+++T E GKPL A+ E+ Y A FL WF+EEA+R+YG+ I ++ Sbjct: 62 LYRAHQLMREQQEELARLMTREQGKPLAAARIEVAYGADFLLWFAEEAKRIYGETIPSAR 121 Query: 172 KDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQL 231 ++R LV +PVGV +TPWN+P +MITRKV ALAAGCTVV+KPAE TP +A+AL ++ Sbjct: 122 SNQRFLVQHRPVGVVGAVTPWNYPVSMITRKVAPALAAGCTVVLKPAEATPLTAMALFRI 181 Query: 232 ANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRV 291 AG P G N++ + + +GE CT+PLV K++FTGSTA GK L AA +KRV Sbjct: 182 FAAAGAPAGCVNLV--TAAEPAPIGEEFCTNPLVRKLTFTGSTAVGKQLATLAAPQLKRV 239 Query: 292 SMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAEA 351 SMELGG APFIVF A+ A GA KF N GQ C+C NR V R I + FV + Sbjct: 240 SMELGGHAPFIVFADADPVHAAKGAALVKFLNTGQACICPNRIYVHRSILEPFVQTLLDR 299 Query: 352 MKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG----KRHQSGGNF 407 + ++R GNG ++G GPL+N+ A++KV+ V DAV +GA+++ GG R G F Sbjct: 300 I-TAMRAGNGLDQGVQVGPLVNQAALDKVDAQVRDAVDRGASLLCGGHRLTDRGLDQGTF 358 Query: 408 FEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIW 467 + PTLL+ V +ML EETFGPVA VI FD ++ +A+AN D GLA Y Y++D + Sbjct: 359 YAPTLLTGVRPEMLIYREETFGPVAAVIPFDDRDDIIAMANDTDYGLAAYVYTRDLKRAL 418 Query: 468 RVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVK 516 R EQL+ GMVG+N+ +S PFGG+K SGLGREG++ G++EYL+V+ Sbjct: 419 RSFEQLQFGMVGINDINPTSAAAPFGGIKLSGLGREGARLGLEEYLDVR 467 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: 541 Number of extensions: 18 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: 473 Length adjustment: 34 Effective length of query: 489 Effective length of database: 439 Effective search space: 214671 Effective search space used: 214671 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