Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_008507152.1 BIBO1_RS11605 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000182725.1:WP_008507152.1 Length = 483 Score = 518 bits (1333), Expect = e-151 Identities = 263/476 (55%), Positives = 340/476 (71%), Gaps = 8/476 (1%) Query: 46 LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LL+ V GRW+ T V +PA G+ +GTV V + A+ A+ A S W Sbjct: 9 LLKSQCLVNGRWIDAADGTTIKVTNPADGSVIGTVPSLSVATIKEAIDASAKALSGWAAK 68 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KER+ +LRKW+DL+I N D++A I+T+E GKPL EA+GE+LY+A F+EWF+EEA+RVY Sbjct: 69 TAKERAGILRKWFDLIIANADDIALIMTSEQGKPLAEARGEVLYAASFIEWFAEEAKRVY 128 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD I +R V++QPVGV + ITPWNFP+AMITRK ALAAGCT++V+PA+ TP Sbjct: 129 GDTIPAPQNGQRLTVIRQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMIVRPADLTPL 188 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 +ALAL LA +AGIP GV ++ KA+E+G L ++ V K+SFTGST G++L+ Sbjct: 189 TALALGVLAEKAGIPAGVLQIV---TGKAREIGAELTSNDTVRKLSFTGSTEVGRLLMAQ 245 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 A ++KR+S+ELGG APFIVFD A++D AV GAM SK+RNAGQTCVC+NR VQRG++D Sbjct: 246 CAPTIKRISLELGGNAPFIVFDDADLDAAVDGAMVSKYRNAGQTCVCANRIYVQRGVYDK 305 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A A K L+VGNG E G GP+I EKA+ KV+ H+ DAV+KGA ++ GGK + Sbjct: 306 FAEKLA-AKVKELKVGNGTEPGVVIGPMIEEKAITKVKAHIEDAVSKGAKLIAGGK--EL 362 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 GG FFEP +L+ VT DML EETFGP+AP+ FD EEE +A AN GLA YFY+++ Sbjct: 363 GGLFFEPGILTGVTSDMLVAKEETFGPLAPLFAFDTEEEVIAQANDTIFGLAAYFYTENF 422 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519 ++ RV+E LE GMVG N GLIS+ PFGGVKQSGLGREGSKYGI+EYLE KY+C Sbjct: 423 SRAIRVSEALEYGMVGHNTGLISNEVAPFGGVKQSGLGREGSKYGIEEYLETKYIC 478 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: 605 Number of extensions: 24 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: 483 Length adjustment: 34 Effective length of query: 489 Effective length of database: 449 Effective search space: 219561 Effective search space used: 219561 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