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 SMc02780 SMc02780 succinate-semialdehyde dehydrogenase [NADP+] protein
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Smeli:SMc02780 Length = 484 Score = 337 bits (864), Expect = 5e-97 Identities = 186/465 (40%), Positives = 261/465 (56%) Query: 12 LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71 L+ W++A I+V NPATG+ IGRV G AD A+ AA + W A ER+ Sbjct: 14 LVGETWIEADPKNAIEVNNPATGEIIGRVPKLGAADTRTAIEAAARVQKEWAARTAKERS 73 Query: 72 ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131 A +R+ L+ E D + +++T EQGKPL EA E++ A IEWFA+E RRVYG +VP Sbjct: 74 AVLRRWFELMIENKDDLGRILTMEQGKPLAEATGEIVYGASFIEWFAEEARRVYGDLVPG 133 Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191 + V+K+P+G VAA TPWNFP + RK ALA GC+ ++K +TP S A+ Sbjct: 134 HQKDKRILVMKQPIGVVAAITPWNFPNAMITRKAGPALAAGCAMVLKPAAQTPFSAIAIA 193 Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251 AG+P G+ ++ G EI + + +P +RK+TFTGST VG +L + +K+ Sbjct: 194 VLAERAGMPKGLFSVITGSAREIGAEMTSNPTVRKLTFTGSTEVGAELYRQSAATIKKLG 253 Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311 +ELGG+AP IV +DAD+ AV+ A AKFRN GQ C+ R V + + + F+ L + Sbjct: 254 LELGGNAPFIVFDDADLDAAVEGALIAKFRNNGQTCVCANRIYVQDGVYEAFSDKLAQAV 313 Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371 LK GNG+E+G LG L + L + + +A GA + GG R G F+ TV+ Sbjct: 314 AKLKTGNGMEDGVILGPLIDQPALKKVEEHVADALAKGARVVQGGRRHSLGGTFYEATVL 373 Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431 A+V V E FGPVA + F + IA+AN FGLA Y + + A V + + L Sbjct: 374 ADVTQAMAVAREETFGPVAPLFRFKDESDVIAQANDTEFGLASYFYAKDLARVFRVAEAL 433 Query: 432 EVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 E GM+ +N E PFGGVK SG G EG +E ++ K V Sbjct: 434 EYGMVGVNTGLISTAEAPFGGVKLSGLGREGSKYGIEEFMEIKYV 478 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: 616 Number of extensions: 29 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: 484 Length adjustment: 34 Effective length of query: 447 Effective length of database: 450 Effective search space: 201150 Effective search space used: 201150 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