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_011782022.1 MVAN_RS24505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000015305.1:WP_011782022.1 Length = 482 Score = 335 bits (860), Expect = 2e-96 Identities = 188/471 (39%), Positives = 262/471 (55%), Gaps = 3/471 (0%) Query: 9 TQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAH 68 T L I GE S T V++P+ + + VA A D AL AA + W PA Sbjct: 12 TGLWIGGEERQGTS--TFSVLDPSDDEVLATVADATADDARDALDAACAVQGEWAATPAR 69 Query: 69 ERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRI 128 +R +R + RAD IA LMT E GK E++ EV A+ WFA+E R+ GR Sbjct: 70 KRGEILRSVFETITARADDIAALMTLEMGKVFAESKGEVTYGAEFFRWFAEEAVRIEGRY 129 Query: 129 VPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPA 188 P + V K+ VGP A TPWNFP+ RK+ A A GC+ +VK +ETP + Sbjct: 130 TPAPAGTGRILVTKQAVGPCYAITPWNFPLAMGTRKMGPAFAAGCTMIVKPAQETPLTML 189 Query: 189 ALLRAFVDAGVPAGVIGLV-YGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHM 247 L + +AG+P GV+ ++ +P ++ LI +RK+TFTGST VGK L + + Sbjct: 190 LLAKLMAEAGLPKGVLSVLPTSNPGAVTEALINDGRLRKLTFTGSTGVGKALVKQSADKL 249 Query: 248 KRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRAL 307 R +MELGG+AP IV +DADV AV A AK RN G+ C + R V N++R+EFT Sbjct: 250 LRTSMELGGNAPFIVFDDADVDAAVDGAILAKMRNGGEACTAANRIHVANAVREEFTEKF 309 Query: 308 VKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFA 367 VK +G GL+E +TLG L N +++ + ++ +A GA++ GG G GNF+ Sbjct: 310 VKRMSEFTLGKGLDEKSTLGPLINAKQVATVTELVSDAVSRGATVAVGGVAPGGPGNFYP 369 Query: 368 PTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLL 427 TV+ +VP DA + E FGPVA I GFD EE IA AN +GLA Y +T+S + Sbjct: 370 ATVLTDVPADARILKEEVFGPVAPIAGFDTEEEGIAAANDTEYGLAAYVYTQSLDRALRV 429 Query: 428 TQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 + +E GM+ +N+ PFGG+K+SG+G EGG E +E YL TK + + Sbjct: 430 AENIESGMVGVNRGVISDAAAPFGGIKESGFGREGGTEGIEEYLDTKYIAL 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: 596 Number of extensions: 18 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: 482 Length adjustment: 34 Effective length of query: 447 Effective length of database: 448 Effective search space: 200256 Effective search space used: 200256 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