Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate HSERO_RS22910 HSERO_RS22910 benzaldehyde dehydrogenase
Query= curated2:A8A0T8 (492 letters) >FitnessBrowser__HerbieS:HSERO_RS22910 Length = 487 Score = 203 bits (516), Expect = 1e-56 Identities = 153/482 (31%), Positives = 236/482 (48%), Gaps = 25/482 (5%) Query: 7 GDWITG-QGASRVKRNPVSGEVLWQGNDAGAAQVEQACRAARAAFPRWARLSLAERQVVV 65 G W+ QGA+ ++ P +G L Q A V + A AA W + ER + Sbjct: 19 GQWVAAAQGATVLE--PATGRPLTQVGLASPDDVSASVELAIAAQAAWVAMPPRERADIF 76 Query: 66 ERFAGLLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPD 125 R AGL + EL ++ARETG ++ EV I ++ G+ P Sbjct: 77 RRAAGLFHQHFDELARMVARETGGVLFKGEHEVREAITLCHLAAGMPLQAQGQLLPSTPG 136 Query: 126 GAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM-RLW 184 + R P GV+ V P+NFP L + PAL AGN ++ KP TP SG ++ R++ Sbjct: 137 RLSIARRAPLGVIGVISPFNFPLILTLRTVAPALAAGNAVVVKPDLRTPVSGGFMLARIF 196 Query: 185 QQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEM 244 +QAGLP G+L+++ GG ETG+AL + + FTGS G ++ +L+G+ K L+LE+ Sbjct: 197 EQAGLPAGLLHVLPGGAETGEALVTAPGVPMIAFTGSPAVGRRIG-ELAGRHLKKLSLEL 255 Query: 245 GGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQR 304 GG N L+I E AD+D A A++ GQ C A R+L+ + + + L RL ++ Sbjct: 256 GGANALVILEDADLDVAASHAAWGAWLHQGQICMAANRILVHASLE-EGLLQRLADKARH 314 Query: 305 LTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRTLLAPR---LLQSETSL--LT 359 L G+ Q +G +I E+ Q+V Q+ A G + + R L T L + Sbjct: 315 LPVGD-GASGQVALGPMIDERQLQRVHALVQESVAAGAQLVAGGRYEQLFYQPTVLGGVR 373 Query: 360 PGIIEMTGVAGVPDEEVFGPLLRVWRYDSFEEAILMANNTRFGLSCGLVSPEREKFDQLL 419 PG+ V +EE+FGP+ V R+D+ E+AI +AN GL+ G++SP + + Sbjct: 374 PGM-------RVFEEEIFGPVASVIRFDNDEDAIALANRHAGGLAAGVLSPSVGRAMAVA 426 Query: 420 LEARAGIVNWNKPLTGAASTAPFGGIGASGNHR----PSAWYAADYCAWPMASLESDSLT 475 R G+V+ N PFGG G +GN P+ W +Y W ++ ++ Sbjct: 427 ARLRQGMVHVNDQTVNDECVNPFGGPGIAGNGASVGGPADW--EEYTQWRWTTIRQQAMP 484 Query: 476 LP 477 P Sbjct: 485 YP 486 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: 687 Number of extensions: 44 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: 487 Length adjustment: 34 Effective length of query: 458 Effective length of database: 453 Effective search space: 207474 Effective search space used: 207474 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