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 AO356_30285 AO356_30285 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30285 Length = 490 Score = 411 bits (1056), Expect = e-119 Identities = 219/477 (45%), Positives = 299/477 (62%), Gaps = 4/477 (0%) Query: 1 MANVTYTDTQLLIDGEWV-DAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGF 59 +A+ + L IDGEW+ D S +V++P+T + V A ADL R LAAA+ GF Sbjct: 10 IADADHPRVGLFIDGEWIFDRPS--CFEVLDPSTEASLTSVPGATTADLKRVLAAAERGF 67 Query: 60 EAWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFAD 119 + WR P ER + +A A VR R++ IAQ++T+E GK + +AR EV +A +W Sbjct: 68 KIWRDTPPAERNIIISRAIAGVRSRSEEIAQIITRENGKLIADARAEVERSASFFDWDMA 127 Query: 120 EGRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKA 179 + R YG IVP Q++++++P+GPVAAFTPWN P++ RK+S AL GCS ++KA Sbjct: 128 QALRAYGTIVPGE-AQMQKSILRQPIGPVAAFTPWNVPLSAPSRKISGALCAGCSIILKA 186 Query: 180 PEETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQL 239 PEETP + A+++ F AG+P GV+ LV+G+PA +SS LI PV R VT TGS VGK L Sbjct: 187 PEETPGAAVAMVQCFERAGLPKGVLNLVFGNPALVSSTLIESPVTRMVTLTGSVAVGKHL 246 Query: 240 ASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSI 299 + LAG MK MELGGHAPVIV E + A K A +K R Q C +P RFLVH SI Sbjct: 247 SQLAGAAMKPVLMELGGHAPVIVCEGVNAAEIGKMALKSKIRINAQWCAAPGRFLVHESI 306 Query: 300 RDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERI 359 DEF A V A+ ++V +G++ +G + + RRL AM +D+A G + GG R+ Sbjct: 307 YDEFVAAFVATADQVRVADGMDTKADIGPVTSVRRLAAMQHFVDDALARGGKVAVGGHRV 366 Query: 360 GSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTR 419 G G +FAPT++ + PLD + +EPFGPVA F L+EAI +N L GLA +AFT Sbjct: 367 GERGYYFAPTLLVDTPLDCAIMTDEPFGPVAVAVRFSTLDEAIEISNSLSVGLAAFAFTN 426 Query: 420 SFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 S L++ L+VG+L IN P P+ PFGGVKDSG G EGGP +L+ Y+V+K+V Sbjct: 427 SLEQAERLSRELDVGVLSINHFGAPDPDTPFGGVKDSGIGREGGPWSLDSYMVSKTV 483 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: 597 Number of extensions: 31 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: 481 Length of database: 490 Length adjustment: 34 Effective length of query: 447 Effective length of database: 456 Effective search space: 203832 Effective search space used: 203832 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