Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_012708927.1 NGR_RS23205 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000018545.1:WP_012708927.1 Length = 477 Score = 239 bits (611), Expect = 1e-67 Identities = 171/472 (36%), Positives = 231/472 (48%), Gaps = 28/472 (5%) Query: 6 IDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 I G WV G G A+ NP TN+ V E A ASA+D A+A+A+ AF AWS + R Sbjct: 8 IAGEWVGGDG--IANVNPSNTNDVVGEYARASAEDASAAIAAAKAAFPAWSRSGILERHA 65 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 I+++ A ++ RK+ L ++ RE GK L E E + D GE + Sbjct: 66 ILRKTADEILARKDELGRLLSREEGKTLAEGIGETIRASQIFDFFAGECLRLAGETLPSV 125 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 + V + P GVV + P+NFP +P I PAL GNTVVFKP+EL PG + A V+ Sbjct: 126 RPNIGVEISREPVGVVGIITPWNFPIAIPAWKIAPALAYGNTVVFKPAELVPGCSWAIVD 185 Query: 184 IWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTG---TLLHKQFGGRPEI 239 I AGLP GVLNLV G+ G A+ + + + FTGS+ TG L + + Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTGTGKRVALASVEHNRK--- 242 Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRG-------AFG 292 LEMGG NP VV + D+ AV A+ SAF S GQRCT + R++V G A G Sbjct: 243 -FQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRVIVTEGIHDKFVAAMG 301 Query: 293 DRFVARLADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQR 352 +R + D A K + Q + A + A+ G E+ R Sbjct: 302 ERMKGLVVDDALKAGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGG-------ELISR 354 Query: 353 D-PALGFVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411 D P A + TN + EE FGP+A ++R D ++A+ ANDT FGLSAG+ Sbjct: 355 DTPGFYLQPALFTEATNAMRISREEIFGPVAAVIRVKDYEEALNVANDTPFGLSAGIATT 414 Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462 + F+R AG+V N PT G PFGG G S R YAA++ Sbjct: 415 SLKHATHFKRNSEAGMVMVNLPTAGVDFHVPFGGRKGSSHGPREQGKYAAEF 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: 514 Number of extensions: 17 Number of successful extensions: 3 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: 477 Length adjustment: 34 Effective length of query: 453 Effective length of database: 443 Effective search space: 200679 Effective search space used: 200679 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