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 H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Burk376:H281DRAFT_03540 Length = 479 Score = 372 bits (955), Expect = e-107 Identities = 204/462 (44%), Positives = 273/462 (59%), Gaps = 2/462 (0%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 I GEW + AS T V+NPATG+ I +VA G + +A+AAA+ F AWR + A ER+A Sbjct: 11 IGGEWYEGAS--TYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRSLTAKERSA 68 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 +++ L+ E DA+A L+T+EQGKPL EAR EV AA EWFA+E +R YG ++P Sbjct: 69 RVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSP 128 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 N A+ V +EPVG VAA TPWNFP+ + RK ALA GC+ ++K EETP S AL Sbjct: 129 NPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSALALAV 188 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 AG+P GV +V GD I L V+RK++FTGST VGK LA + +K+ ++ Sbjct: 189 LAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSL 248 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 ELGG+AP IV +DAD+ AV+ A +KFRN GQ C+ RF V + I D FT AL + A Sbjct: 249 ELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTLALAQAAR 308 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372 ++VGN L+ G L N LT + + + +A + GA + TG + G F+ PTV+ Sbjct: 309 KMRVGNALQGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGTFYEPTVLV 368 Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432 + + E FGPVAA F +EA+A AN PFGL+ Y +TR A + + LE Sbjct: 369 DASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARAWRVGEALE 428 Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 GM+ IN+ PFGGVK SG G EG L+ Y K Sbjct: 429 SGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEYTELK 470 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: 608 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: 479 Length adjustment: 34 Effective length of query: 447 Effective length of database: 445 Effective search space: 198915 Effective search space used: 198915 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: 51 (24.3 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