Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3655 PS417_18705 succinate dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >FitnessBrowser__WCS417:GFF3655 Length = 460 Score = 635 bits (1637), Expect = 0.0 Identities = 310/458 (67%), Positives = 371/458 (81%) Query: 5 SATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAAL 64 + THA+S+NP GE V S P+ + +++DAA+ + +R WR+ P++ RA+ L + +AL Sbjct: 3 ATTHALSINPANGETVGSYPYETAQQLDAALDRSTLAFRAWRRQPVSQRAELLLSLASAL 62 Query: 65 RARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEY 124 R + E++AQMITLEMGKPIAQAR E+ K A L +WYA HGPAMLA E TLV+N A IEY Sbjct: 63 REQAEDMAQMITLEMGKPIAQARAEIEKCAQLSEWYAAHGPAMLAPEPTLVDNGSAQIEY 122 Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184 RPLG I AVMPWNFPVWQV+RGAVP +LAGN+Y+LKHAPNVMGSA L+ F AG +G Sbjct: 123 RPLGPIFAVMPWNFPVWQVLRGAVPTMLAGNTYVLKHAPNVMGSAYLIQRAFQKAGFAEG 182 Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244 +F VN TNDGVS+ I D RIAAVT+TGSVRAG AIG+QAGAALKKCVLELGGSDPFIVL Sbjct: 183 LFEVVNVTNDGVSKAIADPRIAAVTLTGSVRAGIAIGSQAGAALKKCVLELGGSDPFIVL 242 Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304 NDADLD AV+AA+ GR+QNSGQVCAA+KR I+E G+ EAFT KF++A AL MGDP Sbjct: 243 NDADLDAAVQAALIGRFQNSGQVCAAAKRLIIEEGVVEAFTVKFLEASRALVMGDPTSAA 302 Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364 Y+GPMARFDLRDELH QV ATL+EGATLLLG K+ GAGNYY PTVL +VT MT F+Q Sbjct: 303 TYIGPMARFDLRDELHGQVQATLEEGATLLLGGHKVPGAGNYYEPTVLADVTDQMTSFKQ 362 Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424 ELFGPVA++ TARDADHA+ALANDSEFGL+A+++TTD A+A+ A +LE GG+F+N + Sbjct: 363 ELFGPVASIITARDADHAVALANDSEFGLTASIFTTDSAKARDIANQLETGGIFINAFSV 422 Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462 SD RVAFGGVKKSGFGRELSHFG+ EFCNAQTVW DR+ Sbjct: 423 SDPRVAFGGVKKSGFGRELSHFGVREFCNAQTVWLDRK 460 Lambda K H 0.319 0.133 0.392 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: 574 Number of extensions: 10 Number of successful extensions: 1 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: 462 Length of database: 460 Length adjustment: 33 Effective length of query: 429 Effective length of database: 427 Effective search space: 183183 Effective search space used: 183183 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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