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 AO353_28230 AO353_28230 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28230 Length = 485 Score = 348 bits (893), Expect = e-100 Identities = 191/463 (41%), Positives = 266/463 (57%), Gaps = 1/463 (0%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 IDG+W+ A + T+DV++PA G+ + RV + RA+ AA+ + AWR PA ERAA Sbjct: 18 IDGQWIGADNAATLDVIDPANGQLLARVPAMQGTETRRAIDAAEKAWPAWRARPAAERAA 77 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 + + + + D +A +MT EQGKPL EA+ E+ A ++WFA+E RRVYG +P Sbjct: 78 LLERWYQAMIDNLDDLALIMTCEQGKPLNEAKGEIRYGAGFVKWFAEEARRVYGETIPAP 137 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 + + +K+PVG AA TPWNFP + RK + ALA GC +VK + TP S AL Sbjct: 138 SGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCPIIVKPSDLTPLSALALAV 197 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 G+PAGV ++ G PA I L +P +RK++FTGST VG+ L + H+KR ++ Sbjct: 198 LAERVGIPAGVFNVLTGMPAGIGEELTGNPSVRKISFTGSTAVGRLLMRQSAEHIKRLSL 257 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 ELGG+AP IV +DAD+ AV +KFRNAGQ C+ R LV + I + F + LV+ Sbjct: 258 ELGGNAPFIVFDDADLEQAVAGIMLSKFRNAGQTCVCANRILVQDGIYERFAQRLVEEVG 317 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372 LKVGNGL+ T+G L NP ++ +A ID+A GA + GG G + F PTV+ Sbjct: 318 KLKVGNGLDADVTIGPLINPAAVSKVARHIDDALSQGARLLCGGIPEG-DSQFVQPTVLG 376 Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432 + + N E FGPVA + F + EA+A AN P+GL Y FT+ + LE Sbjct: 377 DAHAGMLLANEETFGPVAPLMRFTEEAEALALANATPYGLGAYYFTQDLRRSWRFGEALE 436 Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKS 475 GM+ +N PFGG+K SG G EG L+ YL K+ Sbjct: 437 FGMVGLNTGIISMEVAPFGGIKQSGLGREGSKYGLDEYLEVKA 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: 665 Number of extensions: 33 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 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