Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate AO353_24475 AO353_24475 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24475 Length = 477 Score = 520 bits (1339), Expect = e-152 Identities = 255/471 (54%), Positives = 334/471 (70%) Query: 11 LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70 L I G W + ++I V+NPAT + IG +A A +AD++ A AA+ GF W++V A ER Sbjct: 6 LFIGGVWRNTHPDESIPVINPATEEQIGLIAKASLADIEDAAIAAEKGFATWKQVSALER 65 Query: 71 AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130 A M KAA+L+RERA+ IA ++T E GKPL EA EV + AD I+W A+EGRR YGR++P Sbjct: 66 ATIMHKAASLIRERAENIALILTTEHGKPLGEAMGEVAATADTIDWHAEEGRRAYGRVIP 125 Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190 R LG Q V EP+GPV F PWNFP+ Q V+K++ ALA GCS ++K E P L Sbjct: 126 SRALGVHQFTVMEPIGPVVGFAPWNFPLIQAVKKVAGALAAGCSIILKGATEAPTCAVEL 185 Query: 191 LRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRA 250 ++AF DAGV G + L++GD +IS +LI HP IRKVTFTGSTPVGK+LASLAGLHMKR+ Sbjct: 186 VKAFADAGVSPGAVNLLFGDSGQISEHLIAHPSIRKVTFTGSTPVGKKLASLAGLHMKRS 245 Query: 251 TMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKH 310 TMELGGHAPVIV +DAD+A AVK + AK+RNAGQVC+SPTRFLVH+ + DEF V+ Sbjct: 246 TMELGGHAPVIVMDDADIATAVKISVAAKYRNAGQVCVSPTRFLVHSKVFDEFVSRFVEG 305 Query: 311 AEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTV 370 A + VG+GL+ T+G +A+ RL A ++ +A GA +ETGG RIG +G FF PTV Sbjct: 306 ARAVMVGDGLDPNVTMGPMAHAGRLKATEELVADAVSHGAKLETGGNRIGHKGYFFEPTV 365 Query: 371 IANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQR 430 + NVP+ A +EPFGP+A I FD ++EAI EANRLP+GL+ YA+TRS ++ + L Sbjct: 366 LTNVPVTARAMIDEPFGPIALINSFDDIDEAIKEANRLPYGLSAYAYTRSLSSANKLFNG 425 Query: 431 LEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 +E G + IN + PE PFGGVKDSGYG+EGGP AL+ ++ TK V++ +V Sbjct: 426 IESGAISINHHSVALPEHPFGGVKDSGYGTEGGPGALDAFMTTKFVSLASV 476 Lambda K H 0.318 0.134 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: 660 Number of extensions: 22 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: 481 Length of database: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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 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