Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= SwissProt::Q9SAK4 (528 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 284 bits (726), Expect = 6e-81 Identities = 170/479 (35%), Positives = 256/479 (53%), Gaps = 25/479 (5%) Query: 53 TQGLIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTAG 112 T+ I G W+D T+ V NPAT E+ ++ + + A+ ++ +AF S+S+ + Sbjct: 5 TKFYIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAFASFSQTSRE 64 Query: 113 ERSKVL--------RRWYDLLIAHKEELGQLITLEQGKPLKEAIGEVAYGASFIEYYAEE 164 ER +L +R+ D+ A EE+G L Q IG V A+ ++ Y E Sbjct: 65 ERIDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQTAAAVLKGYKFE 124 Query: 165 AKRVYGDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPS 224 R I+ K+P+GV ITPWN+P+ I KVGPA+A+GCT+V+KPS Sbjct: 125 EDRGTTRIV------------KEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPS 172 Query: 225 ELTPLTALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLM 284 E+ P + E+ AGVP G N+V G+ P +G AL P+V ++FTGST G ++ Sbjct: 173 EIAPFSGYIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVA 232 Query: 285 AAAAPTVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIY 344 AAPTVK+V ELGG +P+I+ DDAD AV G +A+ NSGQ+C R+LV Sbjct: 233 KNAAPTVKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARM 292 Query: 345 DKFAEAFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHS 404 D+ A + VGD GP++++ K++ +Q + +GA ++ GG Sbjct: 293 DEVIAIAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRP 351 Query: 405 LGMT---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIF 461 G+ + +PTV +V++ M ++KEEIFGPV ++ + T ++A+ + NDT GLAAY+ Sbjct: 352 EGLDKGYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVS 411 Query: 462 TNSVQRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIKYV 520 +V L G V +N G +APFGG K SG GRE + E+LE K + Sbjct: 412 GGDQDEVRKVASRLRAGQVTLN-GAGPDLMAPFGGYKMSGNGREWGDHAFGEFLETKAI 469 Lambda K H 0.317 0.134 0.383 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: 551 Number of extensions: 19 Number of successful extensions: 5 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: 528 Length of database: 479 Length adjustment: 34 Effective length of query: 494 Effective length of database: 445 Effective search space: 219830 Effective search space used: 219830 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: 52 (24.6 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