Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_012385751.1 BIND_RS14275 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000019845.1:WP_012385751.1 Length = 478 Score = 368 bits (945), Expect = e-106 Identities = 197/471 (41%), Positives = 283/471 (60%), Gaps = 12/471 (2%) Query: 52 FVGGRWL--PTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERS 109 F+ G W + + V DPA+GA LG VA + A+ A A SW+ R+ Sbjct: 8 FIDGAWRVGTSKESIDVLDPATGASLGEVASADTADVEEAIAVASVALKSWRATPAWTRA 67 Query: 110 SLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYT 169 LL D+M +E A+IIT ESGKPL +A+ E S WF+EE RR+YG I+ + Sbjct: 68 DLLHAVADVMRDRLEEAARIITLESGKPLAQARREWNLSIDQFRWFAEETRRIYGRIVES 127 Query: 170 SAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALA 229 A R +L +PVG+ + T WNFP+ ++ RK+ ALAAGC+V+V+P+++ P +A+ L Sbjct: 128 RAPGGRIEILHEPVGIVAAFTAWNFPAVLVARKIAPALAAGCSVIVRPSDECPGTAMHLV 187 Query: 230 QLANQAGIPPGVYNVI--PCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANS 287 QAG+P GV N++ P T A L PLV KI+ TGSTA G+ ++ +A + Sbjct: 188 DCLRQAGVPKGVVNLVVGPVKNTYAP-----LVASPLVRKITLTGSTAVGQQMIRDSAAT 242 Query: 288 VKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTK 347 VKRVSMELGG AP IVFD +VD + A +K+ NAGQ CV +RF V IHD F+ Sbjct: 243 VKRVSMELGGNAPLIVFDDVDVDAVLDIATPTKYGNAGQICVAPDRFYVHESIHDRFIEG 302 Query: 348 FAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR--HQSGG 405 A+ K+LR+G+G ++ T GPLIN++ ++ +E V DA ++G + TGG+R Q+ G Sbjct: 303 LAQ-RAKALRLGHGLDDATQMGPLINQRRIDAMESIVADAESRGGRIATGGQRPAGQNKG 361 Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465 FF PT++S + + + EE FGP+A V F E ANA++ GLA Y +++DPA+ Sbjct: 362 FFFAPTVISGLPDNAKALAEENFGPIAAVTPFSDPESVYERANASEFGLAAYVFTRDPAR 421 Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVK 516 + ++E GMV VN +++ E PFGG+K SG+GREG GI ++L VK Sbjct: 422 MREAVSRIETGMVAVNSTALAAAEAPFGGIKFSGMGREGGSEGILDFLNVK 472 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: 578 Number of extensions: 25 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: 478 Length adjustment: 34 Effective length of query: 489 Effective length of database: 444 Effective search space: 217116 Effective search space used: 217116 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