Align Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized)
to candidate Ga0059261_1006 Ga0059261_1006 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P9WNX9 (457 letters) >FitnessBrowser__Korea:Ga0059261_1006 Length = 453 Score = 444 bits (1141), Expect = e-129 Identities = 235/453 (51%), Positives = 292/453 (64%), Gaps = 4/453 (0%) Query: 5 TINPATGETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQRARWANATADLLEAEADQ 64 +INPATGE TF A DD ++AA+ RA F +R + AQR A AD EA Sbjct: 4 SINPATGEAGATFAALDDDAIEAALTRAEAAFRSWRASDIAQRTALLTAIADRFEANKRH 63 Query: 65 AAAMMTLEMGKTLAAAKAEALKCAKGFRYYAENAEALLADEPADAAKVGASAAYGRYQPL 124 A T EMGKTLA+A AE KC GFR+YA+ LA P + K + A G + PL Sbjct: 64 LAETATKEMGKTLASAIAEVEKCIAGFRHYADKGPGYLA--PIET-KTASGRAVGHWLPL 120 Query: 125 GVILAVMPWNFPLWQAVRFAAPALMAGNVGLLKHASNVPQCALYLADVIARGGFPDGCFQ 184 G ILAVMPWNFP WQ VR+ AP ++AGNVGLLKHAS CA + +++ G PDG FQ Sbjct: 121 GPILAVMPWNFPYWQVVRWLAPTILAGNVGLLKHASLTQGCAALIQQMVSAAGAPDGLFQ 180 Query: 185 TLLVSSGAVEAILRDPRVAAATLTGSEPAGQSVGAIAGNEIKPTVLELGGSDPFIVMPSA 244 L + S V I+ D RVAA TLTGSE AG V AG +K VLELGGSDPFIVMPSA Sbjct: 181 NLPIKSDKVSRIIADTRVAAVTLTGSEGAGAKVAEAAGRALKKVVLELGGSDPFIVMPSA 240 Query: 245 DLDAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRVGDPTDPDTDV 304 DLD AV+TAV RVQN GQSCI AKR IVHAD+YD F+DKF A M A+++GDP + ++ Sbjct: 241 DLDKAVATAVKARVQNAGQSCICAKRMIVHADVYDAFLDKFTAAMLAVKIGDPMEDGVEM 300 Query: 305 GPLATEQGRNEVAKQVEDAAAAGAVIRCGGKRLDRPGWFYPPTVITDISKDMALYTEEVF 364 GPL++ + R+ V +QVE A A GA + GG +++R G + V+T + D EE+F Sbjct: 301 GPLSSVEQRDTVLEQVERAVADGATL-AGGAKIERDGAWMEAGVLTHVHPDADFAQEEIF 359 Query: 365 GPVASVFRAANIDEAVEIANATTFGLGSNAWTRDETEQRRFIDDIVAGQVFINGMTVSYP 424 GPVA VFRA +ID A+ +AN FGLGS+ WT D+ E RF+ DI +G +N + S P Sbjct: 360 GPVAMVFRADDIDAAIALANDVPFGLGSSVWTSDQAEIDRFVRDIESGMTAVNQLLASTP 419 Query: 425 ELPFGGVKRSGYGRELSAHGIREFCNIKTVWIA 457 E PFGGVK SG+GREL G+ EF N+K V +A Sbjct: 420 EAPFGGVKLSGHGRELGPWGLHEFMNLKAVMLA 452 Lambda K H 0.319 0.133 0.393 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: 462 Number of extensions: 12 Number of successful extensions: 3 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: 457 Length of database: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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 Apr 09 2024. 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