Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__psRCH2:GFF374 Length = 480 Score = 243 bits (619), Expect = 1e-68 Identities = 174/470 (37%), Positives = 243/470 (51%), Gaps = 21/470 (4%) Query: 5 FIDGAWVDGAGPVFASRNPGT-NERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63 FIDG WV G+ A+ NP ++ + E A A A VE+A+A+ARRAF AW+ + AR Sbjct: 10 FIDGQWV-GSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWATFGIQARA 68 Query: 64 TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123 +++ ++ R+E L T++ RE GK L EA EVA + GE Sbjct: 69 DALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLRQAGETLQS 128 Query: 124 MADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATV 182 + GV V + P GV+ + P+NFP +P I PAL GN VV KP++L PG A A Sbjct: 129 VRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLVPGCAWAIA 188 Query: 183 EIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVL 241 EI AG PAGV NLV G+ ++ G A+ N + +D + FTGS G + + R V Sbjct: 189 EIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTCVARGAKV- 247 Query: 242 ALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLAD 301 LEMGG NP +V + D++ AV QSAF S GQRCT + RI+V G + DRFV + + Sbjct: 248 QLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIY-DRFVEAMVE 306 Query: 302 VASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEM-----KQRDPAL 356 KI V A Q G + + + R + +G + + + Sbjct: 307 RIKKI--KVGSALEQ---GVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGTE 361 Query: 357 GFVNAAILDV---TNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDE 413 G+ A L V N+R + EE FGP+A +V+ D D+A+A ANDT FGLSAG+ Sbjct: 362 GYFLAPTLFVDSDPNMR-ISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420 Query: 414 QAWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462 + + F+R +AG+V N PT G PFGG G S R YA ++ Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEF 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: 515 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 487 Length of database: 480 Length adjustment: 34 Effective length of query: 453 Effective length of database: 446 Effective search space: 202038 Effective search space used: 202038 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 Apr 09 2024. 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