Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_5616 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
Query= BRENDA::A6T8Z5 (462 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5616 Length = 463 Score = 628 bits (1619), Expect = 0.0 Identities = 312/463 (67%), Positives = 363/463 (78%), Gaps = 1/463 (0%) Query: 1 MMNLSA-THAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRR 59 M N+S+ THA+S+NP GE + P+ SE ++AA++ A AG+ WR P +R+ +L Sbjct: 1 MTNVSSLTHAISINPANGEQIGYYPFESESALEAALSRAVAGFSLWRSKPAEERSQSLIT 60 Query: 60 IGAALRARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQ 119 + LR E +A MITLEMGKP QARGE+ K A LC+WYAEHGPAML E T VE + Sbjct: 61 LAKVLRGNAETMANMITLEMGKPTTQARGEIEKCAQLCEWYAEHGPAMLTAEPTQVEGGK 120 Query: 120 AVIEYRPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAA 179 A IEYRPLG ILAVMPWNFP+WQV+RGAVP L+AGN+Y+LKHAPNVMG A LL E F A Sbjct: 121 ARIEYRPLGPILAVMPWNFPIWQVLRGAVPALIAGNTYVLKHAPNVMGCAYLLREAFKQA 180 Query: 180 GLPDGVFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSD 239 P+GVF +N T DGVS I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSD Sbjct: 181 DFPEGVFEVINVTPDGVSTAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSD 240 Query: 240 PFIVLNDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGD 299 PFIVLNDADLDEAVKAAV GRYQN+GQVCAA+KR I+E GI EAFTRKFV+A L +GD Sbjct: 241 PFIVLNDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIVEAFTRKFVEATRELVVGD 300 Query: 300 PRDEQNYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGM 359 P Y+GPMARFDLRDEL +QV TL+EGATLL+G +K EG+GN++ PTV +VT M Sbjct: 301 PLATDTYIGPMARFDLRDELDRQVQQTLEEGATLLMGGKKAEGSGNFFEPTVFADVTDRM 360 Query: 360 TGFRQELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFL 419 T F+QELFGPVA++ TARDA HAL LANDSEFGL++T+YT D A + A ELE GGVF+ Sbjct: 361 TSFKQELFGPVASIITARDAAHALELANDSEFGLASTIYTRDVELAHKLAGELETGGVFI 420 Query: 420 NGYCASDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462 NGYCA+D RV FGGVKKSGFGRELSHFG+ EFCNAQTVW DRR Sbjct: 421 NGYCATDPRVTFGGVKKSGFGRELSHFGVREFCNAQTVWLDRR 463 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: 13 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: 463 Length adjustment: 33 Effective length of query: 429 Effective length of database: 430 Effective search space: 184470 Effective search space used: 184470 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