Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate PfGW456L13_495 Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
Query= curated2:A8A0T8 (492 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_495 Length = 480 Score = 199 bits (507), Expect = 1e-55 Identities = 148/463 (31%), Positives = 225/463 (48%), Gaps = 14/463 (3%) Query: 4 WINGDWITGQGASRVK-RNPVSGEVLWQGNDAGAAQVEQACRAARAAFPRWARLSLAERQ 62 +I+G W+ +K NP +GE+L GAA+ +A AA A P W L+ ER Sbjct: 14 FIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 Query: 63 VVVERFAGLLESNKAELTAIIARETGKPRWEAATEVTAMINKIA-ISIKAYHVRTGEQRS 121 + R+ L+ N+ +L ++ E GKP EA E+ + I + +A + Sbjct: 74 TKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPG 133 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 PD + +P GV A P+NFP + PAL AG T++ KP+ TP+S A+ Sbjct: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALA 193 Query: 182 RLWQQAGLPPGVLNLVQGGR-ETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240 L Q+AG+P GV ++V G + G L++ + L FTGS G QL + + +K+ Sbjct: 194 ELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKV- 252 Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300 +LE+GGN P I+ + AD+D AV I S + GQ C CA RL ++ G DAF +L Sbjct: 253 SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVY-DAFAEKLKV 311 Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRTLLAPRLLQS---ETSL 357 +L GN E G LI E+A +V + G L + ++ E ++ Sbjct: 312 AVAKLKIGN-GLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPMEGNFFEPTI 370 Query: 358 LTPGIIEMTGVAGVPDEEVFGPLLRVWRYDSFEEAILMANNTRFGLSCGLVSPEREKFDQ 417 LT + A V EE FGPL ++R+ + I M+N+T FGL+ + + + + Sbjct: 371 LT----NVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFR 426 Query: 418 LLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460 + G+V N L + APFGGI ASG R + Y + Sbjct: 427 VAEALEYGMVGVNTGLI-SNEVAPFGGIKASGLGREGSKYGIE 468 Lambda K H 0.318 0.134 0.408 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: 552 Number of extensions: 34 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: 492 Length of database: 480 Length adjustment: 34 Effective length of query: 458 Effective length of database: 446 Effective search space: 204268 Effective search space used: 204268 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