Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 273 bits (699), Expect = 7e-78 Identities = 155/453 (34%), Positives = 254/453 (56%), Gaps = 9/453 (1%) Query: 32 NPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELIIENQDDLA 91 NP TGE + T P AE +A++ A AW+ + R L++ +L+ E+ A Sbjct: 7 NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66 Query: 92 RLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGD--VIPGHQPDKRLIVIKQPIGV 149 +++TLE GK + EA+GE+ A +E++A+ A+++ + H + V P G+ Sbjct: 67 KVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQSWVEHVPQGI 126 Query: 150 TAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALAELAQRAGIPAGVFSVV 209 A+ PWNFP I R A P LAAG ++LK AS P A A L + AG+P G F+ + Sbjct: 127 LLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGFTNL 186 Query: 210 SGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKVSLELGGNAPFIVFDDAD 269 + + + + +P V+ ++ TGS G + ++ + +KK ++ELGG F+V DAD Sbjct: 187 YATRDQLKA-IIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLADAD 245 Query: 270 LDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVAVAKLKIGNGLEAGTTTG 329 LDKAV+ A+ ++ N GQ C + R+ + D +YDAF EK K VA+L+ G+ +E TT Sbjct: 246 LDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPSTTLA 305 Query: 330 PLIDEKAVAKVQEHIADALSKGA--TVLAGGKPMEGNFFEPTILTNVPNNAAVAKEETFG 387 P+ AV +++ + A++ GA V+ P G FF P +L++V ++ E FG Sbjct: 306 PMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYWEFFG 365 Query: 388 PLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVN--TGLISN 445 P++ + R +DEAD I ++ND+ FGL + D+ VA+ + GMV +N TG+ ++ Sbjct: 366 PVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTGVAAD 425 Query: 446 EVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 PFGG++ SG GRE + GI++++ K + + Sbjct: 426 --LPFGGVRRSGYGRELTGLGIKEFVNHKLIAV 456 Lambda K H 0.317 0.135 0.390 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: 507 Number of extensions: 28 Number of successful extensions: 5 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: 480 Length of database: 463 Length adjustment: 33 Effective length of query: 447 Effective length of database: 430 Effective search space: 192210 Effective search space used: 192210 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: 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