Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase
Query= curated2:Q2SXN9 (487 letters) >FitnessBrowser__Phaeo:GFF501 Length = 476 Score = 221 bits (564), Expect = 3e-62 Identities = 157/464 (33%), Positives = 226/464 (48%), Gaps = 12/464 (2%) Query: 6 IDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 I G W + A+ NP T + + A++ A+D+ERA+A+AR A W++ R Sbjct: 7 IAGDWSETVAAA-ANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQQRFD 65 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 ++ ++ RK L ++ RE GK L E E A + GE + Sbjct: 66 VLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEILGSV 125 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 GV V + P GVV + P+NFP +P I PAL G+ VV KP+EL PG A A E Sbjct: 126 RPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAHALAE 185 Query: 184 IWRDAGLPAGVLNLVQGEKDT-GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I +GLP GV N+V G T G L R +D + FTGS +TG+ + G + + L Sbjct: 186 IINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRK-KLQ 244 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NP+VV + D++ AV ++ AF S GQRCT + R++V G DRFVA L + Sbjct: 245 LEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEG-IHDRFVAALGER 303 Query: 303 ASKI-TASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQRDPALGF--V 359 + + + D Q +G V+ R + + G + + GF Sbjct: 304 MTGLRVGNALDDSTQ--IGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYLA 361 Query: 360 NAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHTF 419 A + + +N + EE FGPLA ++R D D+A+ ANDT FGLSAG+ + F Sbjct: 362 PALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHF 421 Query: 420 RRAIRAGIVNWNRPTNGASSAAPFGGA-GRSGNHRPSAYYAADY 462 + AG+ N PT G PFGG G S R +A ++ Sbjct: 422 KAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGAREQGSHAKEF 465 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: 507 Number of extensions: 17 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: 476 Length adjustment: 34 Effective length of query: 453 Effective length of database: 442 Effective search space: 200226 Effective search space used: 200226 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