Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= BRENDA::A0A0J9X1M8 (465 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 396 bits (1018), Expect = e-115 Identities = 205/457 (44%), Positives = 290/457 (63%), Gaps = 4/457 (0%) Query: 1 MAYQTIYPYTNEVLHTFDNMTDQGLADVLERAHLLYKKWRKEDHLEERKAQLHQVANILR 60 M+Y TI PYT E + TF + TD + L++A +++ W K+ + R L + A++LR Sbjct: 1 MSYATINPYTGETVKTFPSATDAEVTQALDQAQAMFEAW-KDVGVAARVKVLQKAADLLR 59 Query: 61 RDRDKYAEIMTKDMGKLFTEAQGEVDLCADIADYYADKADEFLMSTPLET---DSGQAYY 117 +YA+++T +MGK+ EA+GEV+LCA I +YYAD A++ L L + Q++ Sbjct: 60 ESHTQYAKVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWV 119 Query: 118 LKQSTGVILAVEPWNFPYYQIMRVFAPNFIVGNPMVLKHASICPRSAQSFEELVLEAGAE 177 G++LAVEPWNFPYYQI+R+ AP GN ++LKHAS P+ A +FE L EAG Sbjct: 120 EHVPQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLP 179 Query: 178 AGSITNLFISYDQVSQVIADKRVVGVCLTGSERGGASIAEEAGKNLKKTTLELGGDDAFI 237 G TNL+ + DQ+ +I D RV GV LTGSE GA +A +AG+ LKK+T+ELGG DAF+ Sbjct: 180 QGGFTNLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFV 239 Query: 238 ILDDADWDQLEKVLYFSRLYNAGQVCTSSKRFIVLDKDYDRFKELLTKVFKTAKWGDPMD 297 +L DAD D+ + R +NAGQVC SSKR IV+D+ YD F E + GDPM+ Sbjct: 240 VLADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPME 299 Query: 298 PETTLAPLSSAQAKADVLDQIKLALDHGAELVYGGEAIDHPGHFVMPTIIAGLTKDNPIY 357 P TTLAP+SS A D+ Q++ A+ HGA++ G + G F P +++ ++ DNP Sbjct: 300 PSTTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPAR 359 Query: 358 YQEIFGPVGEIYKVSSEEEAIEVANDSNYGLGGTIFSSNQEHAKAVAAKIETGMSFINSG 417 Y E FGPV ++ + E +AI +ANDS +GLGG++F+++ +H VA KI TGM +IN Sbjct: 360 YWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHP 419 Query: 418 WTSLPELPFGGIKHSGYGRELSELGFTSFVNEHLIYI 454 +LPFGG++ SGYGREL+ LG FVN LI + Sbjct: 420 TGVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAV 456 Lambda K H 0.317 0.135 0.392 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: 540 Number of extensions: 17 Number of successful extensions: 3 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: 465 Length of database: 463 Length adjustment: 33 Effective length of query: 432 Effective length of database: 430 Effective search space: 185760 Effective search space used: 185760 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 (21.6 bits) S2: 51 (24.3 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