Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PP_3151 PP_3151 NAD+-dependent succinate semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >FitnessBrowser__Putida:PP_3151 Length = 461 Score = 623 bits (1607), Expect = 0.0 Identities = 310/457 (67%), Positives = 365/457 (79%), Gaps = 2/457 (0%) Query: 5 SATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAAL 64 S THA+S++P +GE + + P+ ++ ++AA+ A GYRQWRQ L R++ L + L Sbjct: 6 SLTHAISLDPYSGEQIGTYPFDTDAALEAALQRAKVGYRQWRQVSLGQRSEYLLALADTL 65 Query: 65 RARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEY 124 A+ E A MI+ E+GKPIAQARGEV+K LC WYAEHGPAMLA E T VE +A IEY Sbjct: 66 EAKAEAFAHMISREIGKPIAQARGEVSKCVGLCRWYAEHGPAMLAAEPTQVE--KARIEY 123 Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184 RPLG ILAVMPWNFPVWQV+RGAVP +LAGN+Y+LKHAPNVMGSA L+ E+F AGLP+G Sbjct: 124 RPLGPILAVMPWNFPVWQVLRGAVPAILAGNTYVLKHAPNVMGSAYLMAELFKDAGLPEG 183 Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244 VF +N T DGV++ IND RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFIVL Sbjct: 184 VFEVLNVTPDGVTRAINDPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFIVL 243 Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304 DADLD AV+AAV GRYQN+GQVCAA+KR I+EA I +AFT KFV+A LK+G+P ++ Sbjct: 244 ADADLDAAVQAAVIGRYQNTGQVCAAAKRLIVEASIVDAFTHKFVEATRQLKVGNPLEDD 303 Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364 Y+GPMAR+DLRDEL QV ATL EGATLLLG K+EG N+YAPTV NVT MT F+Q Sbjct: 304 TYIGPMARYDLRDELDGQVQATLAEGATLLLGGNKVEGVANFYAPTVFANVTPDMTAFKQ 363 Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424 ELFGPVA + TARDADHA+ LANDSEFGL++T+YT D A A+R L+ GGVF+NGYCA Sbjct: 364 ELFGPVAAIITARDADHAVELANDSEFGLASTIYTADYALAERMTAALDTGGVFINGYCA 423 Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDR 461 SD RVAFGGVKKSGFGRELSHFG+ EF NAQTVW DR Sbjct: 424 SDPRVAFGGVKKSGFGRELSHFGVREFTNAQTVWLDR 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: 607 Number of extensions: 16 Number of successful extensions: 2 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: 461 Length adjustment: 33 Effective length of query: 429 Effective length of database: 428 Effective search space: 183612 Effective search space used: 183612 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