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_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 341 bits (874), Expect = 4e-98 Identities = 193/483 (39%), Positives = 273/483 (56%), Gaps = 6/483 (1%) Query: 2 ANVTYTDTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQ 56 A VT D L+ +DG WV A G+ DV++PATG I V G + RA+ AA+ Sbjct: 13 AAVTDLDPSLIKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAE 72 Query: 57 SGFEAWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEW 116 + + WR+ A +RAA M L+ DA+A+L++ EQGKPL EA E+ A I W Sbjct: 73 AAWNPWRQRTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISW 132 Query: 117 FADEGRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFL 176 FA+EG+R YG ++P + V+K+P+G VAA TPWNFP+ + RK + ALA GC + Sbjct: 133 FAEEGKRAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVV 192 Query: 177 VKAPEETPASPAALLRAFVDAGVPAGVIGLVYG-DPAEISSYLIPHPVIRKVTFTGSTPV 235 VK E+TP S AL AG+P G+ +V PA + + + +RK++FTGST V Sbjct: 193 VKPAEDTPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRV 252 Query: 236 GKQLASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLV 295 GK L + +K+ ++ELGG+AP IV +D D+ AV A +K+RN+GQ CI RFLV Sbjct: 253 GKLLMAQCAETVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLV 312 Query: 296 HNSIRDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETG 355 I ++F L + A + VG+ L G L N + +A+ + +A GA + TG Sbjct: 313 QAGIYEDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTG 372 Query: 356 GERIGSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGY 415 G G F+ PTV+A+V F E FGPVA + F+ EAIA AN FGLAGY Sbjct: 373 GRPHALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGY 432 Query: 416 AFTRSFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKS 475 ++R A V + + LE GM+ +N+ PFGG+K+SG G EG L+ ++ TK Sbjct: 433 FYSRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKY 492 Query: 476 VTV 478 V + Sbjct: 493 VCI 495 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: 650 Number of extensions: 30 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: 499 Length adjustment: 34 Effective length of query: 447 Effective length of database: 465 Effective search space: 207855 Effective search space used: 207855 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