Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Pf6N2E2_351 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_351 Length = 482 Score = 212 bits (540), Expect = 2e-59 Identities = 159/462 (34%), Positives = 231/462 (50%), Gaps = 24/462 (5%) Query: 3 ELFIDGAWVDGAGPV-FASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDA 61 + +I+G W+ A P NP T + E A S +DV+RAVA+AR AFA WS+ +DA Sbjct: 14 QFYINGDWLSPAYPATLPVVNPATEHVIAEVARGSGEDVDRAVAAARAAFAGWSSTPVDA 73 Query: 62 RCTIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAK-VDISITAYHERTGEK 120 R I+ + AL++ERKE LA + E G + AR +AA+ V ++ T +K Sbjct: 74 RMAILGKIHALILERKEELAQALSLEMGAAISFARAMQVPLAAEHVRVARDVLSTYTFQK 133 Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180 + G A+ R P GV + P+N+P + + PA+ AG TVV KPSEL+P A Sbjct: 134 ---IEHGTAIQR-EPIGVCGLITPWNWPLYQITAKVAPAIAAGCTVVLKPSELSPLSALL 189 Query: 181 TVEIWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239 ++ DAGLPAGV NLV G + G A+A H ID + TGS+ G L+ + P + Sbjct: 190 FAQLVHDAGLPAGVFNLVNGSGAEVGAAMAAHPDIDLISITGSNRAGALVAQ--AAAPTV 247 Query: 240 V-LALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298 + E+GG +P V+ D AV + SAF + GQ C+ R++VPR +A Sbjct: 248 KRVTQELGGKSPNVLLPDTDFAKAVPSGVMSAFRNVGQSCSAPTRMIVPRNR-----LAE 302 Query: 299 LADVASKITASVFDADPQ---PFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPA 355 + +A+ ++ +PQ +G + + +R+ A + GA + R Sbjct: 303 VEALAAATANAIIVGNPQLEETVLGPIANEAQFNRVQAMIEVGMNEGAKLVCGGPGRPEG 362 Query: 356 L--GFVN--AAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411 L GF V + + EE FGP+ I+ Y +D+A+A ANDT +GL A + Sbjct: 363 LEQGFYTRPTVFSQVDSAMRIAQEEIFGPVLCIIAYDTVDEAVAIANDTVYGLGAHVQGQ 422 Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHR 453 D IRAG V N P + APFGG RSGN R Sbjct: 423 DLDLVRAVASRIRAGQVLLNYP--AWNPMAPFGGYKRSGNGR 462 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: 465 Number of extensions: 32 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