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 WP_090446352.1 BLS63_RS15725 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_900100495.1:WP_090446352.1 Length = 485 Score = 347 bits (889), Expect = e-100 Identities = 189/468 (40%), Positives = 266/468 (56%), Gaps = 5/468 (1%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 Q ++G+W +A SG ++ NPA+G+ IG V + G + RA+AAAQ+ AWR + A E Sbjct: 14 QAYVNGQWCEADSGARTEIRNPASGEIIGSVPNLGRGETRRAIAAAQAAQPAWRALTAKE 73 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 RA +R+ +L+ + +A++MT EQGKPL EAR E+ AA IEWFA+E +R YG ++ Sbjct: 74 RANRLRQWFSLIMANQEDLARIMTAEQGKPLAEARGEIAYAASFIEWFAEEAKRAYGDVI 133 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P + V KE VG AA TPWNFP + RK ALA GC+ L+K +TP S A Sbjct: 134 PAHATDKRILVQKEAVGVTAAITPWNFPSAMITRKAGPALAAGCAMLLKPAPQTPFSALA 193 Query: 190 LLRAFVDAGVPAGVIGLVYGD---PAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLH 246 L AG+PAG+ ++ D ++ L +P++RK++FTGST VG +L Sbjct: 194 LAALAECAGIPAGLFSVLPADVDASRDVGGELCENPIVRKLSFTGSTAVGIRLMQQCAPT 253 Query: 247 MKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRA 306 +K+ ++ELGG+AP IV +DAD+ AV+ A +K+RNAGQ C+ R V + + F Sbjct: 254 LKKLSLELGGNAPFIVFDDADLDAAVEGAIISKYRNAGQTCVCANRLYVQDGVYQAFAAK 313 Query: 307 LVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFF 366 L LKVGNG+EEG T G L N + + + +A GA++ GG +G GNFF Sbjct: 314 LAAAVAKLKVGNGMEEGVTTGPLINAEAVAKVERHLRDALDKGATLVAGGNSLG--GNFF 371 Query: 367 APTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHL 426 PT+++ V + V E FGP+A + F E I +AN FGLA Y + R V Sbjct: 372 EPTIVSGVTAEMAVAREETFGPLAPLFRFSDEAEVIRQANDTEFGLAAYFYARDLGRVFR 431 Query: 427 LTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 + + LE GM+ IN PFGG+K SG G EG L+ YL K Sbjct: 432 VAEALEYGMVGINTGLISTEVAPFGGMKSSGLGREGSKYGLDEYLEIK 479 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: 592 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: 485 Length adjustment: 34 Effective length of query: 447 Effective length of database: 451 Effective search space: 201597 Effective search space used: 201597 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 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