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 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 353 bits (907), Expect = e-102 Identities = 192/463 (41%), Positives = 263/463 (56%), Gaps = 1/463 (0%) Query: 15 GEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATM 74 G W DA SG T V NPA G I V G A+ RA+AAA + + W A +RA + Sbjct: 26 GAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVL 85 Query: 75 RKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNL 134 R+ L+ AD +A+++T E GKPL EAR EV+ A +EWFA+E +R+YG +P Sbjct: 86 RRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPGHLP 145 Query: 135 GAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAF 194 A+ V+++P+G V A TPWNFP+ + RK + ALA GC+FL K E+TP S AL Sbjct: 146 DARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAVLA 205 Query: 195 VDAGVPAGVIGLV-YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATME 253 AG+PAG+ ++ D + I + +RK+TFTGST VG+ L + A +K+ +ME Sbjct: 206 ERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSME 265 Query: 254 LGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEG 313 LGG+AP IV +DAD+ AV+ A KFRNAGQ C+ R V + + D F L E Sbjct: 266 LGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAAVEE 325 Query: 314 LKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIAN 373 LKVG+G EG T+G L N + + +D+ R G ++ TGGE G FF PTV+ Sbjct: 326 LKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTPTVVTG 385 Query: 374 VPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEV 433 V + V E FGPVA + F + +E IA AN FGLAGY + R + +++ LE Sbjct: 386 VTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALEY 445 Query: 434 GMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 G++ IN PFGGVK SG G EG ++ YL K + Sbjct: 446 GIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYI 488 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: 609 Number of extensions: 16 Number of successful extensions: 2 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: 492 Length adjustment: 34 Effective length of query: 447 Effective length of database: 458 Effective search space: 204726 Effective search space used: 204726 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