Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 151 bits (382), Expect = 4e-41 Identities = 149/463 (32%), Positives = 213/463 (46%), Gaps = 26/463 (5%) Query: 5 FIDGAWVDGAG-PVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63 FI G WV G F +R+P + + A + D+E A+ +A A AW + R Sbjct: 22 FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSVTERS 81 Query: 64 TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVD-ISITAYHERTGEKRA 122 ++ + A + + E LA E GK + E T A + VD A R E A Sbjct: 82 NLLLKIADRVEQNLEFLAVAETWENGKAVRE--TLNADLPLFVDHFRYFAGCIRAQEGSA 139 Query: 123 PMADGVAVLRHRPH--GVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 D V H P GVV P+NFP + I PAL AGN +V KP+E P Sbjct: 140 ADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPVSILV 199 Query: 181 TVEIWRDAGLPAGVLNLVQG-EKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 VE+ +D LPAGVLN+V G + G ALA ++I L FTGS+ G + K I Sbjct: 200 MVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILK-CAAESLI 257 Query: 240 VLALEMGGNNPLV----VAEVED--IDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGD 293 +E+GG +P + V E ED +D AV + AF + G+ CTC R+L+ + D Sbjct: 258 PSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLL-AFFNQGEVCTCPSRVLIAESIY-D 315 Query: 294 RFVARLADVASKIT-ASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIE---- 348 +F+ ++ A I + D D Q +GA S ++++ GA +I Sbjct: 316 KFIDKVIARAKTIKQGNPLDTDTQ--VGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSC 373 Query: 349 MKQRDPALGF-VNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAG 407 D + GF + IL N + EE FGP+ + + D +A+A ANDT +GL AG Sbjct: 374 QLSGDQSSGFYIEPTILKGHNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAG 433 Query: 408 LLADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSG 450 + D R I+AG V W + + A FGG +SG Sbjct: 434 VWTRDMNRAQRMGRGIQAGRV-WINCYHAYPAHAAFGGYKKSG 475 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: 496 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: 487 Length of database: 506 Length adjustment: 34 Effective length of query: 453 Effective length of database: 472 Effective search space: 213816 Effective search space used: 213816 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