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_086511804.1 BZY95_RS20815 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_002151265.1:WP_086511804.1 Length = 495 Score = 365 bits (937), Expect = e-105 Identities = 193/462 (41%), Positives = 267/462 (57%) Query: 13 IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72 IDG WVDA+ I+VV+PA+ +G V A + A+ +A W+ A ERAA Sbjct: 27 IDGSWVDASDEAIIEVVDPASDTRLGSVPRLTQAQVREAIESADRALPQWKARTAKERAA 86 Query: 73 TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132 +R+ L + +A+++T EQGKPL EAR E+ + IEWFA+E +R+YG ++P Sbjct: 87 ILRRWYELCMAHQEDLARILTLEQGKPLAEARGEITYGSAFIEWFAEEAKRIYGDVIPAH 146 Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192 + V KEPVG VAA TPWNFP + RK +AA+A GC+ +VK TP S AL Sbjct: 147 AGDRRIVVTKEPVGVVAAITPWNFPNAMITRKAAAAMAAGCTVVVKPASSTPFSALALAE 206 Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252 AGVP GV+ +V G + L +P++RK++FTGST VGK L + +K+ +M Sbjct: 207 LAERAGVPRGVLNVVTGSARTVGDELTANPLVRKLSFTGSTEVGKVLLAACAQTVKKVSM 266 Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312 ELGG+AP I+ +DAD+ AV +KFRN GQ C+ R VH I +F L + Sbjct: 267 ELGGNAPFIIFDDADLDQAVAGVMASKFRNTGQTCVCANRIFVHERIYADFAERLAQAVA 326 Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372 +VGNGLEEG TLG L +P + + I +AR+ GAS+ GG+R GNFF PT++ Sbjct: 327 AQRVGNGLEEGVTLGPLIDPAAVAKVEEHIADARERGASVYLGGQRHALGGNFFEPTILT 386 Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432 +V DA + N E FGPVA + F +E + AN P+GLA Y +TR V + + LE Sbjct: 387 DVSSDARLMNEETFGPVAPLLRFSDEQEVVRLANDTPYGLASYFYTRDVGRVWRVAEALE 446 Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 G++ IN+ PFGGVK+SG G EG +E Y+ K Sbjct: 447 CGIVGINEGIISSELAPFGGVKESGIGREGSKYGIEDYIEIK 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: 670 Number of extensions: 30 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: 495 Length adjustment: 34 Effective length of query: 447 Effective length of database: 461 Effective search space: 206067 Effective search space used: 206067 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