Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_054343024.1 Nant_RS18090 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001305295.1:WP_054343024.1 Length = 487 Score = 540 bits (1392), Expect = e-158 Identities = 263/482 (54%), Positives = 356/482 (73%), Gaps = 6/482 (1%) Query: 44 ADLLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWK 101 A LL+ +++ G+W+ A TF V +PA+G L VA G E R A+ AA A SWK Sbjct: 8 ARLLKTQAYIDGQWVDGDAGDTFAVTNPATGEHLADVASVGWAETRRAINAAQQAMISWK 67 Query: 102 EISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARR 161 + K RS LL +W++L+I+N+++LA ++TAE GKPL E++GE+ Y A F++WF+EE +R Sbjct: 68 ALPAKSRSELLERWFNLVIENQEDLAVLMTAEQGKPLFESRGEVAYGASFIKWFAEEGKR 127 Query: 162 VYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDT 221 VYGDII T D+RG+V+KQPVGV + ITPWNFP+AMI RKV ALA GC +V+KPA +T Sbjct: 128 VYGDIIPTP-NDRRGVVVKQPVGVVAAITPWNFPNAMIARKVAPALAVGCAMVLKPAAET 186 Query: 222 PYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILL 281 P SALAL +LAN+AG+P G+++V+P S A+E+GE + ++P+V K++FTGST GK+L+ Sbjct: 187 PLSALALVELANRAGLPAGLFSVLPSSN--AREIGEEMTSNPIVKKVTFTGSTPVGKLLM 244 Query: 282 HHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIH 341 A++VKR SMELGG AP I+FD A++D AVAG + +K+RN+GQTC+C+NR LVQ GI+ Sbjct: 245 KQCADTVKRTSMELGGNAPVIIFDDADLDAAVAGVLVAKYRNSGQTCICANRILVQEGIY 304 Query: 342 DSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRH 401 D+FV KF A+K RVGNG + +T GP+I EKA +++ V AVA+GATV+ GGK Sbjct: 305 DAFVEKFTAAVK-GFRVGNGMDNNSTHGPVITEKAAAEIDAKVKSAVAEGATVILGGKPG 363 Query: 402 QSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQ 461 G F+EPT+L+NVT M EE FGPVAP+ KF EE+A+A+AN + GLA Y Y++ Sbjct: 364 AQGACFYEPTILTNVTDKMRVFREEIFGPVAPIFKFSTEEQAIAMANDTEFGLAAYLYTE 423 Query: 462 DPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521 + +IWRV+E ++ GMVGVNE ISS PFGGVK+SG GREGSKYG+D+YLE KY+C G Sbjct: 424 NLGRIWRVSEGIDYGMVGVNETAISSEVIPFGGVKESGQGREGSKYGLDDYLETKYICMG 483 Query: 522 GL 523 GL Sbjct: 484 GL 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: 625 Number of extensions: 21 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