Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011811733.1 VEIS_RS19570 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000015565.1:WP_011811733.1 Length = 500 Score = 535 bits (1379), Expect = e-156 Identities = 267/480 (55%), Positives = 350/480 (72%), Gaps = 3/480 (0%) Query: 46 LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105 LL+ D + GRW+ F V DPA+G KL VA+ G +A AA+ AA A+ WK + Sbjct: 16 LLKTDGLIDGRWVAGSRRFDVLDPATGLKLADVANLGPADADAAIAAANAAWGPWKSRTA 75 Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165 KERS +LRKW +L++ ++D+LA+I+TAE GKPL EA+GE+ Y A F+EWF+EEA+R+ G+ Sbjct: 76 KERSIILRKWCELLLAHQDDLARIMTAEQGKPLAEAKGEVGYGASFVEWFAEEAKRINGE 135 Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225 + +R LVL+Q +GV + ITPWNFP AMITRKV ALAAGC V++KPAE TP +A Sbjct: 136 TLPQFDNSRRLLVLRQSIGVCAAITPWNFPLAMITRKVAPALAAGCPVIIKPAELTPLTA 195 Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285 LA A+LA +AGIP GV+N++ + +G+VLC +V ISFTGST G+IL+ +A Sbjct: 196 LAAAELALRAGIPAGVFNILCADGDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSA 255 Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345 +VK++S+ELGG APFIVF A++D AV GA ASK+RNAGQTCVC+NRF VQ ++D FV Sbjct: 256 PTVKKMSLELGGNAPFIVFADADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEAVYDEFV 315 Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKR--HQS 403 KFA A + +VGNGF+ G QGPLI E AV KV++HV DA+AKG VVTGG+R + Sbjct: 316 QKFA-AKVLTAKVGNGFDAGVNQGPLIEEAAVLKVQRHVADAIAKGGRVVTGGQRLPNLG 374 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 G FFEPT+L++ DMLC EETFGP AP+ KF E+EA+A AN + GLA YFYS+D Sbjct: 375 SGQFFEPTVLADARPDMLCAREETFGPFAPIFKFKTEQEAIAAANDTEFGLASYFYSRDL 434 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 +I+RV E LE GMVGVN G++++ PFGGVKQSGLGREGS +GID+Y+E+KY+C G + Sbjct: 435 GRIFRVGEALEYGMVGVNVGILATEHVPFGGVKQSGLGREGSHHGIDDYVEIKYLCLGDI 494 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: 660 Number of extensions: 24 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: 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