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_013834856.1 THICY_RS01540 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000214825.1:WP_013834856.1 Length = 456 Score = 233 bits (593), Expect = 1e-65 Identities = 144/452 (31%), Positives = 232/452 (51%), Gaps = 4/452 (0%) Query: 29 VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW-RKVPAHERAATMRKAAALVRERADA 87 +NPATG+ + LD A+ A + F W ++ R ++ A ++R + D Sbjct: 6 INPATGEKLAEFEAWDQERLDLAIRRANAEFLEWSQRTSLATRCELIKNAGKILRAQQDE 65 Query: 88 IAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVKEPVGP 147 +A+L+T E GK + EA+ E+ +A + +++A+ G + P ++ + +P+G Sbjct: 66 LAKLITLEMGKSINEAKAEIEKSAWVCDFYAEHGPKFLAD-EPIATDASKSYICYQPLGL 124 Query: 148 VAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPAGVIGLV 207 V A PWNFP QV R + AL G L+K P A+ R F++AG+PA V + Sbjct: 125 VLAVMPWNFPFWQVFRFAAPALIAGNIGLLKHASNVPQCAQAIERIFIEAGLPASVFTNL 184 Query: 208 YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVIVAEDAD 267 ++ S +I +R VT TGS P G+++A++AG +K+ +ELGG IV DAD Sbjct: 185 MIGSDKVES-VIRSRYVRAVTLTGSEPAGRKVAAIAGEELKKTVLELGGSDAFIVMSDAD 243 Query: 268 VALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKV-GNGLEEGTTL 326 + AV+AA +++ N GQ CI+ RF+V I ++F L E V G+ L+ TTL Sbjct: 244 IPAAVEAAVTSRYLNMGQSCIAAKRFIVDTFIYEDFITRLKTAVESRFVEGDPLDPATTL 303 Query: 327 GALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVFNNEPF 386 +A L + + GA + TGG ++ G ++APT++A++ ++ E F Sbjct: 304 CPMARQDLLDELHQQVQTCVDYGARLVTGGYQLDRPGCYYAPTILADISSAMPAYHEEFF 363 Query: 387 GPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQPATPWP 446 GPVA I + A+ AN FGL G ++ A + R+E G ++N P Sbjct: 364 GPVALIFKASEPAHAVGLANATQFGLGGSVWSSDGATAETMALRMESGACFVNGMTKSDP 423 Query: 447 EMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 +PFGGVK+SGYG E + + KS+ + Sbjct: 424 RLPFGGVKNSGYGRELSYHGIREFTNIKSIWI 455 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: 536 Number of extensions: 36 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 Apr 09 2024. 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