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_025330278.1 SALWKB2_RS03375 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000600005.1:WP_025330278.1 Length = 456 Score = 232 bits (592), Expect = 2e-65 Identities = 139/452 (30%), Positives = 239/452 (52%), Gaps = 6/452 (1%) Query: 29 VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH--ERAATMRKAAALVRERAD 86 +NP TG+ ++ +++ L A + +++ P + ER A +++ A ++ + Sbjct: 6 INPFTGELARTFSNHTNTEVENVLTQAHALYKSEWSQPENISERQALLQRLAEIMTRHQE 65 Query: 87 AIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVKEPVG 146 IA+++T + GK + E+R E+++ +I++++A + + P LG + V P+G Sbjct: 66 KIARIITLDMGKRIAESRNEIVNCIEIVQYYAKQAAELLKPAAYPSKLG-KGWVEHHPIG 124 Query: 147 PVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGL 206 + A PWNFP+ Q++R ++ A+A G + K P + +A PAG Sbjct: 125 IILAVEPWNFPIYQLIRVIAPAIAVGNPVVAKHASNVPQCAQLVEDLLHEAQAPAGTYTN 184 Query: 207 VYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDA 266 ++ P +I + +I ++ V TGS G +A AG +K++TMELGG+ +V +DA Sbjct: 185 LFVTPEQIET-IIGDKRVQGVALTGSEGAGIIVAGQAGSKLKKSTMELGGNDVFVVTDDA 243 Query: 267 DVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLEEGTTL 326 DV A A + NAGQVCI+ RF+VH + ++FTR + + + +G+ L+E TTL Sbjct: 244 DVVAAAHTAVAGRLFNAGQVCIAAKRFIVHEKVAEQFTRIVQEDFAQVVMGDPLDENTTL 303 Query: 327 GALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPF 386 L++ + + +D A GA + G + ++GNFF PT+I ++ D + E F Sbjct: 304 APLSSRKSKDTLQEQLDAAIAHGAKVICGNK--PAKGNFFTPTLITDISRDNPAYFEEFF 361 Query: 387 GPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWP 446 GPVA + EEAI AN FGL G F++ L R+E GM++IN+ Sbjct: 362 GPVAQLYIVKNDEEAITLANDSNFGLGGTVFSKDIERAKKLASRIETGMVFINRFGDSVA 421 Query: 447 EMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 E+PFGG+K SG+G E ++ ++ K V + Sbjct: 422 ELPFGGIKRSGFGRELSDLGIKEFVNHKLVVL 453 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: 509 Number of extensions: 31 Number of successful extensions: 5 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: 456 Length adjustment: 33 Effective length of query: 448 Effective length of database: 423 Effective search space: 189504 Effective search space used: 189504 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 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