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 HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__HerbieS:HSERO_RS05395 Length = 484 Score = 357 bits (917), Expect = e-103 Identities = 194/465 (41%), Positives = 268/465 (57%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 Q ++G+W DA G+ + V NPA G+ +G V G A+ RA+ AA + + AW+K A E Sbjct: 13 QAFVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAAWPAWKKKTAKE 72 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 R+A +R+ L+ D +A +MT EQGKPL EAR E+ AA IEWFA+EG+R YG + Sbjct: 73 RSAILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFAEEGKRTYGDTI 132 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P + + V+KE +G AA TPWNFP + RK ALA GC ++K E TP S A Sbjct: 133 PSPSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLKPAEATPFSALA 192 Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 L AG+PAGV +V G P I + +P++RK++FTGST VGK L + +K+ Sbjct: 193 LAVLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKLLMQQSASSIKK 252 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 ++ELGG+AP IV +DAD+ AV+ A +K+RNAGQ C+ R V + + D F LV+ Sbjct: 253 LSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDGVYDAFAAKLVE 312 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 + KVG G EEG T G L N + + + + +A GA + GG+R +FF PT Sbjct: 313 AVKKFKVGQGTEEGVTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKRHALGHSFFEPT 372 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 V+A+V V E FGP+A + F EE +A AN FGLA Y ++R + + + Sbjct: 373 VLADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYSRDIGRIWRVAE 432 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 LE GM+ IN PFGGVK SG G EG ++ YLV K Sbjct: 433 GLESGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYLVVK 477 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: 620 Number of extensions: 24 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: 484 Length adjustment: 34 Effective length of query: 447 Effective length of database: 450 Effective search space: 201150 Effective search space used: 201150 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 17 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