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_108401521.1 B9Z44_RS01610 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_003063475.1:WP_108401521.1 Length = 487 Score = 385 bits (989), Expect = e-111 Identities = 204/475 (42%), Positives = 281/475 (59%), Gaps = 3/475 (0%) Query: 6 YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65 YT I+G W + ++ ++NPAT +G + AG + A+AAA + R + Sbjct: 7 YTSHGQFINGTWRAGSESASV-MINPATEISLGEMKPAGAEQVTEAIAAAYEARTSMRAL 65 Query: 66 PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125 A R+A +R+AA + ERA+ + L+ E GKP+ +A E ++A+ ++WFADE RRV+ Sbjct: 66 TAWNRSALLRRAATFINERAEMLGHLVALETGKPIRQAVGEAKASAESVDWFADEARRVF 125 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 G R + V EP+G VAAF PWNFP+ + RK++ ALA G + +++ E Sbjct: 126 GMSYESRVKSDRYLVHMEPLGVVAAFVPWNFPLLLLARKMAPALAAGNTLVIRPSSEAAG 185 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 S AL++ F DAG P GV+ LV G PAEI+ ++ + KV+FTGS P+G+Q+ + + Sbjct: 186 STMALIKCFEDAGFPKGVVNLVIGRPAEITPTIMNDSRVAKVSFTGSVPIGRQIVEQSAI 245 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 +KR +MELGGHAPVIV DAD+ A KFRNAGQVC SPTRF VH SI E Sbjct: 246 TLKRVSMELGGHAPVIVHSDADIDAFAAMAAPGKFRNAGQVCASPTRFYVHESIAKEVEE 305 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGG--ERIGSEG 363 L+ L+VG+ L++ T LG LA RR A+ ++DNA GA + +GG R G Sbjct: 306 KLITATRALRVGSPLDDATDLGPLATRRRRDAIEQLVDNAVSGGARVLSGGMRPRRMDRG 365 Query: 364 NFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423 F+ PT + + DA V N+EPFGP+ + F L++ IAEANRLPF LA Y FTRS Sbjct: 366 YFYEPTWLTQLQPDALVLNDEPFGPIGTLATFSTLDQVIAEANRLPFALAAYVFTRSLTK 425 Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 H RL+ G++ +N E PFGG KDSG+G EGGP A+ YL TK V V Sbjct: 426 THATVDRLQAGVIGVNTFVAATAETPFGGSKDSGFGREGGPHAIRDYLDTKFVNV 480 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: 619 Number of extensions: 22 Number of successful extensions: 2 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: 487 Length adjustment: 34 Effective length of query: 447 Effective length of database: 453 Effective search space: 202491 Effective search space used: 202491 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