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 H281DRAFT_03360 H281DRAFT_03360 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Burk376:H281DRAFT_03360 Length = 493 Score = 388 bits (996), Expect = e-112 Identities = 204/475 (42%), Positives = 285/475 (60%), Gaps = 2/475 (0%) Query: 6 YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65 Y + +LI G W A + +NPAT + +G + A A + A+ AA A RK+ Sbjct: 7 YREHGMLIAGRWQSATADNGQVSINPATEERLGYMPLATPAQVTEAIDAATEASAAMRKL 66 Query: 66 PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125 ER A +R+AA L+RERA +A+++ E GKP+ +A E ++A+ I+WFADE RRV+ Sbjct: 67 TPWERTALLRRAATLIRERAPQLARIVALETGKPIAQATGEANASAESIDWFADEARRVF 126 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 G R G + V EP+G VAAFTPWNFP+ + RK+ ALA G + +++ E Sbjct: 127 GMSYESRVKGGRYLVHYEPLGVVAAFTPWNFPLLLLARKMGPALAAGNAIVIRPSNEAAG 186 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 + L+R FVDAG P G + LV G I+ ++ P + K++FTGS P+G+Q+ ++ Sbjct: 187 ATMGLVRCFVDAGFPEGAVNLVIGKADAITPTVMADPRVAKISFTGSVPIGRQIVEMSAK 246 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 +K+ TMELGGHAPVIV DAD+ A KFRNAGQVC SPTRF +H SI D+ + Sbjct: 247 TLKKVTMELGGHAPVIVHRDADIDAFAHLASLGKFRNAGQVCASPTRFYIHESIFDKTVK 306 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGN- 364 ALV+ + L+VG+ L++ T LG L +R A+ ++D A GAS+ GG R G Sbjct: 307 ALVERSTALRVGDPLQQNTDLGPLTTSKRREAIERLVDEAVSEGASVLCGGRRPSQFGRG 366 Query: 365 -FFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFAN 423 F+ PT+I+N + N+EPFGPV + F ++E I EANRLPF LA Y FTRS N Sbjct: 367 WFYEPTLISNPAPHIGLMNDEPFGPVGTLNRFTTMDEVITEANRLPFALAAYVFTRSMRN 426 Query: 424 VHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 T+RL+ G++ +N E PFGG KDSG+G EGGP A+ YL TK + + Sbjct: 427 TLETTERLQAGVVGVNTFVASTAETPFGGSKDSGFGREGGPNAIRDYLDTKFINL 481 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: 670 Number of extensions: 28 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: 493 Length adjustment: 34 Effective length of query: 447 Effective length of database: 459 Effective search space: 205173 Effective search space used: 205173 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