Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001046645.1:WP_066609128.1 Length = 487 Score = 489 bits (1259), Expect = e-143 Identities = 251/475 (52%), Positives = 332/475 (69%), Gaps = 6/475 (1%) Query: 51 SFVGGRWL--PTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKER 108 +F+GG W+ + AT PV +PA+GA +GTV DCG + AA+ AA AF +WK + +R Sbjct: 15 AFIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFPAWKAQTAGDR 74 Query: 109 SSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIY 168 +++L +W+ L++ N +L +I+TAE GKP+ EA+GEI Y+A F++WF+EE RRV G I+ Sbjct: 75 AAVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEEGRRVDGGIVP 134 Query: 169 TSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALAL 228 ++R LV+K+PVGV++ ITPWNFP+AMITRK ALAAGC VVVKP+E TP++ALAL Sbjct: 135 APEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPSELTPFTALAL 194 Query: 229 AQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSV 288 A+LA +AGIP GV+N++ T +G L P+V K+SFTGST G +L+ A+++ Sbjct: 195 AKLAEEAGIPAGVFNIVTGLPT---AIGGALTASPVVRKLSFTGSTRVGSLLMRQCADTI 251 Query: 289 KRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKF 348 KRVS ELGG AP IVFD A+VD AVA AM SKFRNAGQTCVC+NR LVQ G++D F K Sbjct: 252 KRVSFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVYDQFAEKL 311 Query: 349 AEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFF 408 A A+ +L+V G G+T GPLIN AVEKV+ HV DA++ GAT+ +G F Sbjct: 312 ARAV-SALKVAPGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDATGARFA 370 Query: 409 EPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWR 468 P +L+ TRDM EETFGPVAP+ +F EEE + +ANA GLA YFY+++ + +R Sbjct: 371 TPVILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTENLHRAFR 430 Query: 469 VAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 VAE+LE GMV +N G I+ PFGGVK SGLGREG+ GI+EYLE K GL Sbjct: 431 VAERLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETKAFHIAGL 485 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: 638 Number of extensions: 23 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: 487 Length adjustment: 34 Effective length of query: 489 Effective length of database: 453 Effective search space: 221517 Effective search space used: 221517 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