Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate WP_008990279.1 I215_RS02025 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAK7 (458 letters) >NCBI__GCF_000300875.1:WP_008990279.1 Length = 455 Score = 413 bits (1061), Expect = e-120 Identities = 206/456 (45%), Positives = 298/456 (65%), Gaps = 4/456 (0%) Query: 3 IATIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEA 62 + I+P TG + + + +++ ++ +AF+ +NTSFE+R+R + + E+ Sbjct: 4 VTMINPATGEKIDEYIRIDAAQAADKLNKSHSAFKLWKNTSFEQRSRLFNALGNEFENSK 63 Query: 63 DEVARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQF 122 + A+L EMGKT+ A+ E K A ++ADHA+ +LS A E A +V F Sbjct: 64 ERYAQLATQEMGKTIAQARKEIEKCAWICHYYADHAEEFLSNR----AVETEAQKSYVAF 119 Query: 123 DPLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEG 182 P+GVVLAVMPWN+P +Q +RFAAPA+MAGNTG+LKHASNV CAL L + F + GFP+G Sbjct: 120 QPMGVVLAVMPWNFPFYQVIRFAAPAIMAGNTGVLKHASNVQGCALALEEAFRKSGFPDG 179 Query: 183 AFQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVM 242 F L + DV ++++ + AVTLTGS AAG ++A AG N+K++V+ELGG D ++++ Sbjct: 180 IFTNLNIGSNDVKGVIENPNVVAVTLTGSDAAGRSVASIAGANLKKTVMELGGSDAYLIL 239 Query: 243 PSADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDES 302 AD+++A A + RLQN+GQ+CIAAKRF V ++VY++F LF M A+ GDP +ES Sbjct: 240 DDADLDQATTLATLGRLQNNGQTCIAAKRFIVQQEVYEKFLELFSKKMEAAIMGDPTEES 299 Query: 303 TSFGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYRE 362 + +GPLA R ++H+ V + +GA + GG IP+G+G YYPAT+L VT M + Sbjct: 300 SYYGPLARIDLRDELHQQVEKSIAQGARLVIGGTIPQGKGAYYPATILADVTPGMEAFDN 359 Query: 363 ECFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTA 422 E FGPVA + + Q AI L+N+S FGL S V T++ + A ++AG F+N L Sbjct: 360 ELFGPVASVVRAKDEQHAIDLANNSQFGLGSGVITSNNERGEKVALQLQAGSSFVNKLVV 419 Query: 423 SFPAVPFGGLKDSGYGRELSAYGIREFVNIKTVWTS 458 S P +PFGG+K+SGYGRELS+YGI EFVNIK++W S Sbjct: 420 SDPRLPFGGIKNSGYGRELSSYGIHEFVNIKSIWIS 455 Lambda K H 0.317 0.132 0.386 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: 510 Number of extensions: 20 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: 458 Length of database: 455 Length adjustment: 33 Effective length of query: 425 Effective length of database: 422 Effective search space: 179350 Effective search space used: 179350 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: 51 (24.3 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