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_004314497.1 C665_RS13475 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000310185.1:WP_004314497.1 Length = 486 Score = 370 bits (950), Expect = e-107 Identities = 200/466 (42%), Positives = 270/466 (57%) Query: 9 TQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH 68 T+ +DG+W+DA G T + NPATG+ +G + G A+ RA+AAA + + AWR + A Sbjct: 13 TRCHVDGQWIDADDGATTSIRNPATGEVLGTIPRMGAAETRRAIAAANAAWPAWRALTAG 72 Query: 69 ERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRI 128 RA +R+ L+ + +A LMT EQGKPL EAR EVL AA IEWFA+EG+R+YG + Sbjct: 73 ARAKILRRWFELILANQEDLAVLMTSEQGKPLAEARGEVLYAASFIEWFAEEGKRIYGDV 132 Query: 129 VPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPA 188 +P + V KEP+G AA TPWNFP + RK ALA GC+ ++K +TP S Sbjct: 133 IPGHQPDKRIVVTKEPIGVCAAITPWNFPAAMITRKAGPALAAGCTMVLKPATQTPYSAL 192 Query: 189 ALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMK 248 AL AGVP GV +V G AEI L +P++RK+TFTGST +G +L + +K Sbjct: 193 ALAVLAERAGVPKGVFSVVTGGAAEIGGELTANPIVRKLTFTGSTEIGVKLMAQCAPSVK 252 Query: 249 RATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALV 308 + ++ELGG+AP IV +DAD+ AV+ A +K+RN GQ C+ R LV + + D F L Sbjct: 253 KLSLELGGNAPFIVFDDADLDAAVEGAIASKYRNTGQTCVCANRLLVQDGVYDAFAARLA 312 Query: 309 KHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAP 368 LKVGNGL EG+T G L + + + I +A + GA + GG+R G+FF P Sbjct: 313 AAVARLKVGNGLAEGSTQGPLIDMNAVAKVEEHIADAVEKGARVLAGGKRHALGGSFFEP 372 Query: 369 TVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLT 428 T++A+V V E FGPVA + F EAI AN FGLA Y F S V + Sbjct: 373 TILADVTPAMKVAREETFGPVAPLFRFKDEAEAIRMANDTEFGLAAYFFANSMNRVWRVA 432 Query: 429 QRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 + LE G++ IN PFGG+K SG G EG +E YL K Sbjct: 433 EALEYGIVGINTGIISTEVAPFGGMKSSGLGREGSKYGIEDYLEVK 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: 625 Number of extensions: 23 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: 486 Length adjustment: 34 Effective length of query: 447 Effective length of database: 452 Effective search space: 202044 Effective search space used: 202044 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