Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate WP_179243903.1 B9O00_RS00790 aldehyde dehydrogenase family protein
Query= curated2:Q9AAL5 (472 letters) >NCBI__GCF_900177295.1:WP_179243903.1 Length = 480 Score = 216 bits (550), Expect = 1e-60 Identities = 154/464 (33%), Positives = 221/464 (47%), Gaps = 23/464 (4%) Query: 15 EAIADFAVNDARSIDAACHSARAAFAEWAMTPLAERRAIALRFAETVRARREEIATLIAR 74 + + +A DA A +A AAF W+ + +R I + AR+EE+ L++R Sbjct: 29 DVVGLYAQGDAAQAGQAIDAAAAAFPAWSRSTPQQRFDILDAAGTEILARKEELGRLLSR 88 Query: 75 ETGKPMWEALTEADSVAAKVAISIRAQDERAGERSEPMADAT-ARLAHRPHGVLAVIGPF 133 E GK + E + E AG+R + A P GV+ +I P+ Sbjct: 89 EEGKTLPEGIGETVRAGQIFKFFAGEALRIAGDRIDSTRPGVIAEATREPLGVVGLITPW 148 Query: 134 NFPMHLANGHIVPALLAGNAVVFKPSEKTPACGQLMGELWRAAGLPDHVLTIVIGGGEA- 192 NFP+ + + PAL GN VV KP++ P C + ++ + AGLP V +V+G G Sbjct: 149 NFPIAIPAWKLAPALAFGNCVVMKPADLVPGCAWALADILQRAGLPKGVFNLVMGRGSVV 208 Query: 193 GEALVRHEALDGVLFTGGVQAGRAI-HRALADAPHKILALELGGNAPLVVWDVADIEAAA 251 GEA++ + + FTG V GR + R + K LE+GG P VV D AD+E AA Sbjct: 209 GEAILASPKVAAISFTGSVATGRHVARRCIEGEAMKKFQLEMGGKNPFVVLDDADLEVAA 268 Query: 252 HLIVQSAYVTAGQRCTCARRLILPEGARGDALLEALTMLMDRLVIGGPFQSPAPFMGPVI 311 + + A+ + GQRCT + RLI+ EG D +EALT + L + + +GPV+ Sbjct: 269 NSALNGAFFSTGQRCTASSRLIVTEGIH-DRFVEALTSKLKALKVDNALKEGTQ-IGPVV 326 Query: 312 DAHAAAQVL----AAQDR--MTADGGRPLRLAAVREARSALLSPGLIELTDAPLR--DEE 363 D Q L QD A GG L RE L P L TD +R EE Sbjct: 327 DQRQLDQDLDYIKVGQDEGAKLAWGGERLN----RETEGFYLQPALFTETDNAMRINREE 382 Query: 364 IFGPLLQVRRAADFDAALALANATRFGLAAGLISDDEALYRRFWTSVRAGIVNWNRPTTG 423 IFGP+ V R D+D+ALA+AN T+FGL+AG+ + F + +AG+V N PT G Sbjct: 383 IFGPVASVIRVKDYDSALAVANDTQFGLSAGIATSSLKHAEHFKRNSQAGMVMVNLPTAG 442 Query: 424 ASSAAPFGGVGGSGNHRPSAYYAADYSAYPVAGLESPSPVYRLP 467 PFGG + S+Y A + Y V + Y +P Sbjct: 443 VDYHVPFGG------RKNSSYGAREQGRYAVEFYTTVKTAYAMP 480 Lambda K H 0.320 0.135 0.400 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: 560 Number of extensions: 35 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: 472 Length of database: 480 Length adjustment: 33 Effective length of query: 439 Effective length of database: 447 Effective search space: 196233 Effective search space used: 196233 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: 51 (24.3 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