Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_086511804.1 BZY95_RS20815 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_002151265.1:WP_086511804.1 Length = 495 Score = 551 bits (1420), Expect = e-161 Identities = 275/496 (55%), Positives = 362/496 (72%), Gaps = 8/496 (1%) Query: 32 RRSYVGGPADLHAD--LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEAR 87 +RS +GG D L R +++ G W+ A V DPAS +LG+V + R Sbjct: 4 KRSAIGGRQPQLQDPALFRQHAYIDGSWVDASDEAIIEVVDPASDTRLGSVPRLTQAQVR 63 Query: 88 AAVRAAYDAFSSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILY 147 A+ +A A WK + KER+++LR+WY+L + ++++LA+I+T E GKPL EA+GEI Y Sbjct: 64 EAIESADRALPQWKARTAKERAAILRRWYELCMAHQEDLARILTLEQGKPLAEARGEITY 123 Query: 148 SAFFLEWFSEEARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAAL 207 + F+EWF+EEA+R+YGD+I A D+R +V K+PVGV + ITPWNFP+AMITRK AA+ Sbjct: 124 GSAFIEWFAEEAKRIYGDVIPAHAGDRRIVVTKEPVGVVAAITPWNFPNAMITRKAAAAM 183 Query: 208 AAGCTVVVKPAEDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSK 267 AAGCTVVVKPA TP+SALALA+LA +AG+P GV NV+ S A+ VG+ L +PLV K Sbjct: 184 AAGCTVVVKPASSTPFSALALAELAERAGVPRGVLNVVTGS---ARTVGDELTANPLVRK 240 Query: 268 ISFTGSTATGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQT 327 +SFTGST GK+LL A +VK+VSMELGG APFI+FD A++DQAVAG MASKFRN GQT Sbjct: 241 LSFTGSTEVGKVLLAACAQTVKKVSMELGGNAPFIIFDDADLDQAVAGVMASKFRNTGQT 300 Query: 328 CVCSNRFLVQRGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDA 387 CVC+NR V I+ F + A+A+ RVGNG EEG T GPLI+ AV KVE+H+ DA Sbjct: 301 CVCANRIFVHERIYADFAERLAQAVAAQ-RVGNGLEEGVTLGPLIDPAAVAKVEEHIADA 359 Query: 388 VAKGATVVTGGKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIA 447 +GA+V GG+RH GGNFFEPT+L++V+ D + EETFGPVAP+++F E+E V +A Sbjct: 360 RERGASVYLGGQRHALGGNFFEPTILTDVSSDARLMNEETFGPVAPLLRFSDEQEVVRLA 419 Query: 448 NAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKY 507 N GLA YFY++D ++WRVAE LE G+VG+NEG+ISS PFGGVK+SG+GREGSKY Sbjct: 420 NDTPYGLASYFYTRDVGRVWRVAEALECGIVGINEGIISSELAPFGGVKESGIGREGSKY 479 Query: 508 GIDEYLEVKYVCYGGL 523 GI++Y+E+KY+C GGL Sbjct: 480 GIEDYIEIKYLCMGGL 495 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: 681 Number of extensions: 22 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: 495 Length adjustment: 34 Effective length of query: 489 Effective length of database: 461 Effective search space: 225429 Effective search space used: 225429 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