Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_001592305.1:WP_068168204.1 Length = 485 Score = 223 bits (568), Expect = 1e-62 Identities = 168/470 (35%), Positives = 234/470 (49%), Gaps = 24/470 (5%) Query: 5 FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 FI+G V+G G VF S NP T A+ DDV RAV +A FA WSA+ R Sbjct: 9 FINGQTVNGGGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFALWSAMSATERGR 68 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEART-EVASMAAKVDISITAYHERTGEKRAP 123 I++R A +L ER LA + R+ GKP+ EA +V S A ++ A TG++ P Sbjct: 69 ILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQQY-P 127 Query: 124 MADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 + + A R P GV G +N+P + PAL AGN ++FKPSEL P A E Sbjct: 128 LKNAFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLAE 187 Query: 184 IWRDAGLPAGVLNLVQGEKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLAL 243 ++ +AG+P GV N+VQG G LA H + + TGS TG + + G + V + Sbjct: 188 VYLEAGVPPGVFNVVQGRGAVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGTLKRV-TM 246 Query: 244 EMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADVA 303 E+GG +PL+V + D++ AV A+ F + G+ CT R+ V RG RF+ARL + Sbjct: 247 ELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRG-IAPRFLARLKE-- 303 Query: 304 SKITASVFD-ADPQPFMGAVISARAASRLV-------AAQARLVGLGASPIIEMKQRDPA 355 + V D DP +GA+IS +R++ A A LV G +E Sbjct: 304 RTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVE------G 357 Query: 356 LG--FVNAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADD 412 LG FV I D + + EE FGP+ ++ + +AIARAN + F L+AG+ D Sbjct: 358 LGDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTD 417 Query: 413 EQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAADY 462 Q H IRAGI W N PFGG G SG ++ A D+ Sbjct: 418 LQRGHRVAAQIRAGIC-WINNYNITPIEMPFGGVGESGIGSENSMAALDH 466 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: 447 Number of extensions: 23 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: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 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