Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_054341789.1 Nant_RS11485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001305295.1:WP_054341789.1 Length = 493 Score = 539 bits (1388), Expect = e-157 Identities = 268/478 (56%), Positives = 353/478 (73%), Gaps = 5/478 (1%) Query: 46 LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LL+ +F+ G+W + F V +PA+GA L V+D G E A+ AA A+ +W+ Sbjct: 17 LLQTQAFIDGQWCEANSGQRFTVSNPANGAPLAEVSDLGTDEVLQAISAAERAWPNWRAH 76 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER ++LR+W++L++ K++LA ++TAE GKPL EA+GE+LY A F+EWF+EEA+R+Y Sbjct: 77 TGKERGAILRRWFELILAAKEDLAILMTAEQGKPLNEARGEVLYGASFVEWFAEEAKRLY 136 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GDII +DKR +VLKQP+GVA+ ITPWNFP AMITRKV ALAAGC VV+KP+E TP Sbjct: 137 GDIIPAHGRDKRLMVLKQPIGVAAAITPWNFPIAMITRKVAPALAAGCPVVIKPSELTPL 196 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA+LA +AG P GV+NV+ + T A EVG +LC D V K+SFTGST GK+L Sbjct: 197 SALALAKLAQEAGFPDGVFNVV--TSTNAPEVGRILCADSRVRKLSFTGSTPVGKLLAQQ 254 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A +VK+VS+ELGG APFIVFD A++D AV GAM SKFRNAGQTCVC+NR VQ ++++ Sbjct: 255 CAANVKKVSLELGGNAPFIVFDDADLDAAVVGAMVSKFRNAGQTCVCTNRIFVQENVYEA 314 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F KF A+ ++L+ GNG +EG GPLI+E+A+ KVE V DA+ GAT++TGGKR + Sbjct: 315 FAEKFRVAV-EALKTGNGADEGVEIGPLIDERALAKVESLVADALENGATLLTGGKRFSA 373 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 N ++PT+LSNV M EE FGPVA +I F E E +A+AN GLA YFY++D Sbjct: 374 VSNGYQPTVLSNVNNQMRIAQEEIFGPVATLIPFQSESEVIAMANDTPSGLAAYFYARDI 433 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 ++WRV+E LE GMVGVNEG+IS+ PFGG+K+SGLGREGSKYGID+Y+E+KY+C G Sbjct: 434 GRVWRVSEALEYGMVGVNEGIISTEVAPFGGIKESGLGREGSKYGIDDYVELKYICLG 491 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: 641 Number of extensions: 20 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: 493 Length adjustment: 34 Effective length of query: 489 Effective length of database: 459 Effective search space: 224451 Effective search space used: 224451 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