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_012169296.1 AZC_RS03905 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000010525.1:WP_012169296.1 Length = 484 Score = 357 bits (917), Expect = e-103 Identities = 200/463 (43%), Positives = 268/463 (57%) Query: 12 LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71 LI+G W AAS I V NPA G +G V +++ A+ AAQ+ F W + A ER+ Sbjct: 15 LINGAWRKAASNAHIVVHNPANGALVGHVPDLSASEVREAVDAAQAAFGPWSRKAAKERS 74 Query: 72 ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131 A +R+ L+ AD +A LMT EQGKPL EA+ EV+ AA IEWFA+EG+RVYG ++P Sbjct: 75 ALLRRWFDLIIANADDLAALMTAEQGKPLAEAKGEVVYAASFIEWFAEEGKRVYGDVIPA 134 Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191 + V+K+PVG AA TPWNFP + RK + ALA GC ++K E+TP + AL Sbjct: 135 PTTDKRLIVLKQPVGVTAAITPWNFPAAMITRKAAPALAAGCVMIIKPAEQTPLTALALG 194 Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251 +AG+PAGVI +V GD E+ L V+RK++FTGST VG+ L S +KR + Sbjct: 195 VLAQEAGIPAGVIQVVTGDAREVGGVLTGSDVVRKLSFTGSTEVGRILMSQCAPTIKRLS 254 Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311 +ELGG+AP IV +DAD+ AV+ A +K+RNAGQ C+ RF V +SI D F L + Sbjct: 255 LELGGNAPFIVFDDADLEAAVEGAIASKYRNAGQTCVCANRFYVQSSIYDAFAARLAERV 314 Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371 + L VG G E G +G L + + + + + +A + GA+I GG+ G F+ PTV+ Sbjct: 315 KQLPVGVGTEPGVLIGPLIDEDAIAKVKAHVADAVEKGATIALGGKMHALGGTFYEPTVL 374 Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431 V D V E FGPVA + F+ EEAI AN FGLA Y FT + + + L Sbjct: 375 TGVTSDMRVAREETFGPVAPLFRFETEEEAIFLANNTEFGLAAYFFTENARRAWRVAEGL 434 Query: 432 EVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 E GM+ N PFGGVK SG G EG +E YL K Sbjct: 435 EYGMVGHNTGLISNEVAPFGGVKQSGIGREGSKYGIEEYLEIK 477 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: 636 Number of extensions: 24 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 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