Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_068173812.1 HTA01S_RS16360 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_001592305.1:WP_068173812.1 Length = 483 Score = 217 bits (553), Expect = 6e-61 Identities = 158/463 (34%), Positives = 219/463 (47%), Gaps = 8/463 (1%) Query: 5 FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64 FI+G W G ++ T E V E A A + E A+ +A A WS R Sbjct: 13 FINGRWEIGTTTGVSTNPSDTREVVAEYARADRNQTELAIRAAADALPHWSQSSPQRRAD 72 Query: 65 IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124 ++ + + L+ RK+ L ++ RE GK L E EVA GE A + Sbjct: 73 VLDQIGSELLARKDELGALLAREEGKTLPEGVGEVARAGQIFKFFAGEALRIPGEVIASV 132 Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183 GV V + P GVV + P+NFP +P I PAL GNTVVFKP+EL P A E Sbjct: 133 RPGVRVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAE 192 Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242 I GLPAGV NLV G ++ G L +H ++ L FTGS TG + K R + Sbjct: 193 IISRCGLPAGVFNLVMGSGREVGQTLVDHPLVNALSFTGSVSTGERILKAATAR-RAKVQ 251 Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302 LEMGG NPLVV D+D AV A+Q ++ S GQRCT + R++V + D FVA+L Sbjct: 252 LEMGGKNPLVVLADADLDQAVDCALQGSYFSTGQRCTASSRLIV-QAQVHDAFVAKLRQR 310 Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPII--EMKQRDPALGFVN 360 S + + MG V+ + +A GA + ++ QR +++ Sbjct: 311 LSTLKVG-HALERGTEMGPVVDRAQLEQNLAYIEIARNEGAEHVWGGDLLQRPTPGHYMS 369 Query: 361 AAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHTFR 420 A+ + EE FGP+A ++R D + A+ ANDT FGL AG+ + F+ Sbjct: 370 PALFLAKPEHRVAREEIFGPVACVLRADDYEHALVLANDTPFGLCAGICTTSLKYAMHFK 429 Query: 421 RAIRAGIVNWNRPTNGASSAAPFGGAGRSGN-HRPSAYYAADY 462 R G+ N PT G PFGG S + R YA ++ Sbjct: 430 RHAEVGMTMVNLPTAGVDFHVPFGGRKESSHGSREQGRYAVEF 472 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: 549 Number of extensions: 26 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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