Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate BWI76_RS05620 BWI76_RS05620 NAD-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__Koxy:BWI76_RS05620 Length = 482 Score = 212 bits (540), Expect = 2e-59 Identities = 153/463 (33%), Positives = 227/463 (49%), Gaps = 8/463 (1%) Query: 3 ELFIDGAWVDGAGP-VFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61 + I+G W D +G A NP + + A + A+ +A RA AW AL Sbjct: 12 QAMINGRWRDASGKETLAVTNPANGQPLGNVPKMGAGETREAIDAAARALPAWRALTAKE 71 Query: 62 RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEK- 120 R +I++R+ L++E ++ LA ++ E GKPL EA+ E++ A+ ++ G+ Sbjct: 72 RSSILRRWFELMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTI 131 Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 AD ++ +P GV A P+NFP + PAL AG T+V KP+ P A A Sbjct: 132 PGHQADKRLLVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPFSALA 191 Query: 181 TVEIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 E+ AG+P GV N+V G + G L + + L FTGS++ G L +Q + Sbjct: 192 LAELANRAGIPEGVFNVVTGSASEVGGELTGNPLVRKLSFTGSTEIGRQLMEQCAKDIKK 251 Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARL 299 V +LE+GGN P +V + D+D AV A+ S F +AGQ C CA R+ V + DRF +L Sbjct: 252 V-SLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDSVY-DRFAEKL 309 Query: 300 ADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALGFV 359 SK+ P +G +I +A +++ A +G GA + K + F Sbjct: 310 QQAVSKLQIG-DGLQPNVTIGPLIDEKAIAKVQEHIADALGKGARVVTGGKAHELGGNFF 368 Query: 360 NAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHT 418 IL DV ++ EE FGPLA + R+ D D IA+ANDT FGL+A A D Sbjct: 369 QPTILVDVPGDAKVAKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLGRVFR 428 Query: 419 FRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461 A+ GI+ N ++ APFGG SG R + Y + Sbjct: 429 VGEALEYGIIGINTGLI-STEVAPFGGVKSSGLGREGSKYGIE 470 Lambda K H 0.320 0.134 0.402 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: 498 Number of extensions: 24 Number of successful extensions: 4 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: 487 Length of database: 482 Length adjustment: 34 Effective length of query: 453 Effective length of database: 448 Effective search space: 202944 Effective search space used: 202944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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